The BIDMC Multidisciplinary Clinical Informatics Fellowship Program is a 2-year ACGME-accredited training program. For over 40 years, the training program has trained leaders who will transform healthcare through the creative use of information and communication technology. Through real-world exposure to and participation within one of the world's preeminent clinical computing system environments, our fellows learn how to assess the needs of clinicians and patients, refine clinical processes, and design and implement clinical systems. Each fellow is expected to complete a capstone project that demonstrates their mastery of clinical informatics.

Fellows are encouraged to obtain a Masters in Biomedical Informatics, offered through the Department of Biomedical Informatics at Harvard Medical School.

United States citizens and permanent residents can apply for stipends, tuition, and travel funds, typically for two- to three-year periods. The Harvard Medical School Department of Biomedical Informatics (DBMI) is in charge of managing a training grant from the National Library of Medicine (NIH) that supports these funded positions.  Fellows can also work clinically in their specialty in collaboration with one of our participating clinical departments.

Application information is below. See also our Former Informatics Fellows page.

For more information about the Boston-area Biomedical Informatics Research Training Program, please visit the website here.

Policies & Procedures


BIDMC Fellows are governed by the hospital's BIDMC GME Policies. In addition to the institution-wide program policies, informatics fellows are governed by the following clinical informatics-specific policies:

Clinical Informatics Milestones

The Milestones are designed only for use in evaluation of the fellow in the context of their participation in ACGME-accredited fellowship programs. The milestones provide a framework for assessment of the development of the fellow in key dimensions of the elements of physician competency in a subspecialty. 

The BIDMC fellowship program extends the ACGME Clinical Informatics milestones with the addition of institution-specific milestones that represent our approach to informatics training. You can download these below:


The BIDMC ACGME-accredited Multidisciplinary Clinical Informatics Fellowship is a 2-year training program that follows the BIDMC academic calendar

The fellowship consists of didacticscore and elective rotations, coursework, and a capstone project

Some fellows elect to take additional coursework at Harvard's Master's program in Biomedical Informatics, the Harvard School of Public Health in research methodology (Clinical Effectiveness Program), Harvard Business School, or the Massachusetts Institute of Technology.

Fellows have a maximum of 80 hours of work related to fellowship and clinical care (including any moonlighting). 


Through didactics, fellows will learn the fundamentals of health information technology administration and management, with particular focus on the role that informatics serves the organization beyond computerized medical records or providing order entry. There will be a lot of focus on how clinical systems change how care is given and how the switch to electronic health records has affected clinician satisfaction and patient outcomes.

Combined Harvard ACGME Clinical Informatics Lectures Series

Fellows participate in the Combined Harvard ACGME Clinical Informatics weekly lecture series and monthly Grand Rounds, which is a series co-sponsored by the three Harvard Clinical Informatics fellowship programs and the Harvard Department of Biomedical Informatics.

BMI 720 - Clinical Informatics I

  • Class Number:17479
  • Course ID:208203
  • Consent:No Consent
  • Enrolled:12/25
  • Waitlist:0/4

This course provides a detailed overview of clinical informatics for professionals who will work at the interface of clinical care, information technology, and the healthcare system. Students will learn how to analyze, design, implement, and evaluate information and communication technologies found in hospitals, physician offices, and other healthcare settings including the home. Emphasis will be placed on the evolution of the electronic health record and its use to promote patient care that is safe, efficient, effective, timely, patient-centered and equitable. Students will also study implementation failures and unintended consequences of systems. The course will cover the fundamental concepts in clinical informatics such as evidence-based care and clinical workflow analysis. Students will not only study health information systems but have assignments to evaluate some real-life systems at local hospitals. Through case-based analysis, students analyze the life-cycle management of complex clinical computing systems. This course is geared towards physicians seeking postgraduate training. Course director permission required for cross-registration.

Students who are not in the Master of Biomedical Informatics program who wish to cross-register for this course must submit a  petition in my.harvard that summarizes their interest in the course. Cross-reg petitions will be reviewed on a first-come, first-served basis beginning August 25, 2023. Students can and should submit petitions before this date, but they will not be approved ahead of time. 

For questions regarding cross-registration, please contact rebecca_fitzhugh@hms.harvard.edu with the subject line "BMI 720 cross-registration". 

See the course listing on the Harvard Medical School course catalog.

IN 601.0 - Medicine and Management

This joint course between Harvard Medical School and Harvard Business School provides an overview of the structure and function of healthcare institutions and illustrates the role of these organizations in producing successful clinical outcomes. Class sessions, assigned readings, and written assignments offer a multidisciplinary perspective combining the component academic disciplines of management and medicine.  (See the course listing on the Harvard Medical School course catalog.)

Overview: As practicing professionals, physicians continually face complex challenges relating to the organizations in which they work. This class is for students in the HMS/HBS combined MD/MBA program and the Clinical Informatics Fellowship Program. It gives an overview of how healthcare institutions are structured and how they work, as well as the role that these institutions play in achieving good clinical outcomes. Class sessions, assigned readings, and written assignments offer a multidisciplinary perspective combining the component academic disciplines of management and medicine.

Location: Harvard Business School

Prerequisites: completion of HMS PCE for MD students. Member of MD/MBA program or permission of the course directors.

MMSc students in the Biomedical Informatics program are approved to enroll pending course capacity.

IN 590 - Introduction to Health Care Management

Faulty: Holly Khachadoorian-Elia and Stan Finkelstein

2024 Spring - Full Term  = 1/29/2024 to 5/6/2024

  •  Class Number:18534
  • Course ID:217968
  • Consent:Instructor
  • Enrolled:0/55
  • School:Harvard Medical School
  • Department:Program in Medical Education
  • Subject:IN
  • Units:2
  • Course Component:Discipline Specific
  • Grading Basis:HMS Pre-Clinical
  • Cross Reg: Available for Harvard Cross Registration
  • Instruction Mode:In Person
  • Curriculum Phase:Preclerkship
  • Visiting Clerks:NO
  • Course Type:Nonclinical Electives

Introduction to the academic disciplines of business management with illustration from examples in various medical care settings.  Topics include: economics of health care; evolving role of physicians and other medical professionals; ethics of business decisions in a clinical context; underlying concepts in financial, marketing, and operations management in health institutions; and the management of risk in health-related enterprise.  Presentations by carefully selected multidisciplinary faculty group from the Harvard and MIT communities, guest faculty will include managers with experience in health services and medical products related organizations.  Student projects will address current issues occasioned by the rapidly changing health care management environment.

This course is for first year HMS and HSDM students, especially those planning to apply for or considering the MBA joint degree.

Up to 6 HMS Graduate Education students allowed.

See the course listing on the Harvard Medical School course catalog.)

Follow the Order Series

In the Follow the Order series, fellows follow how an order is generated at the point of care and how it is processed and fulfilled downstream. In this series, fellows also learn how EHR's are used in various clinical departments, how they function, and how clinical care processes are supported. The following is an example of some of the sessions in the series:

    • Ambulatory EHR
    • Inpatient EHR
    • Emergency Department Dashboard
    • Critical Care
    • Perioperative and Anesthesia
    • Radiology / RIS
    • Clinical Pathology / Laboratory / LIS
    • Pharmacy
    • Admit / Discharge / Transfer system (ADT)
    • Billing and Coding
    • Data Center
    • 3D Printing / Maker Lab

Asynchronous Learning

Core concepts in clinical informatics will be delivered via professionally created video lectures by our faculty through our online learning portal (only available within the intranet). Faculty-moderated small group sessions will reinforce these fundamental concepts in clinical informatics. Examples of video lectures include:

    • The Field of Clinical Informatics: Introduction to Informatics and core content of the Curriculum
    • A History of Computing at BIDMC: Lessons from 45 years of clinical computing
    • Back to the Future: LINC with Tomorrow: 1967 video with Dr. Warner Slack for the forerunner of PBS Nova
    • Introduction to Databases: Intro to Databases, SQL, NoSQL, Relational, and Hierarchical
    • Global Communities of Practice Module: Using communication technology to link communities across distance and time
    • Health Information Exchange: Clinical Document Architecture Module: Learn about the Clinical Document Architecture, consolidated CDA, and how data can be exchanged electronically between systems.
    • Patient Portals: Patient portals are tools patients can use to access their data.
    • Big Data: The Four V's: Introduction to the meaning of "big data" and the four "V"s
    • Usability of Electronic Health Records Module: Usability Assessment
    • Intro to Natural Language Processing (NLP): NLP is a technology for a computer to parse human language and extract concepts.

Self-Directed Learning

As part of a trainee's individualized learning plan, fellows will undertake self-directed learning depending on their interests and abilities. Some fellows will undertake additional coursework in research methodology, machine learning, computer programming, management, and other topics. This can be fulfilled through online coursework as well as traditional courses through any of the Harvard Graduate Schools (medical, business, public health, etc.) as well as at MIT.


Over the 2-year fellowship, trainees will rotate through core and elective rotations. These rotations will give fellows broad exposure to different parts of the health care enterprise, as well as work with various team members to see how pieces of technology fit together, see how processes connect with one another, and see how data flows between systems. Specific rotations will offer further specific opportunities for working in teams, with a focus on improving safety and quality.

Core Rotations

    • Emergency Informatics
    • Pathology Informatics
    • Radiology Informatics
    • Health Care Quality / Quality Improvement
    • Commercial Vendor EHR's (Meditech, EPIC, Cerner)
    • Information Systems
    • Data Science

Elective Rotations

    • Public Health / Bio-surveillance
    • Population Health
    • Bioinformatics
    • Patient-Facing Informatics / Consumer Informatics

Longitudinal Experiences

Governance Committees

Fellows will participate in the longitudinal governance committee at the medical center during their 24 months of their training program. This will allow them to develop clinical skills and work with frontline clinicians to improve workflow through technology and process engineering. Examples of governance committees that fellows participate in are:

  • outpatient governance committee
  • inpatient governance committee
  • patient health record (patient site) governance committee

Capstone Project

The fellows' training experience will culminate in the completion of a capstone project at the end of their training experience. This capstone project must include a rigorous component of evaluation. 

Examples of possible scholarly activity include, but are not limited to, analysis of existing data marts to understand the clinical use of information systems and the consequences of changes in information systems to clinical outcomes; interventions as part of the electronic medical record the focus on improving quality of care and patient safety through multidisciplinary teams; usability testing and design improvement of health information technology interfaces for frontline clinicians; interventions using consumer health informatics to record and capture patient data and facilitate patient engagement; development of patient-reported outcomes reporting tools that use patient portals and consumer health informatics to collect store and transmit data to clinicians.  In addition, the training program’s faculty has research projects supported by NIH, HHS, private foundations, industry, and international sovereign funds.  Fellows can participate in any of these activities and are encouraged to work in these areas as well.


The Balanced Scorecard Approach

Fellows undertake a balanced scorecard approach to self-assessment, identifying where goals have been met, where they are proceeding as planned, and where they are delayed or deficient. These goals cover both core curricular content as well as progress along their scholarly project. 

A core component of the balanced scorecard approach to evaluation is that it focuses on goals and milestones and allows for continual assessment of status. Rotation feedback and feedback during mentorship meetings may then be applied to the instrument.

Faculty Responsibilities

The program director will be responsible for ensuring that fellows have an individualized learning plan in place that combines core curricula, electives, and scholarly activity. The curricula will map to milestones once they are in place for clinical informatics, and these will be reviewed every six months at core competency committee meetings.

Associate program directors who are responsible for overseeing the mentorship of assigned fellows will meet with fellows no less frequently than every four weeks, in which case milestones may be assessed and evaluated in a more continuous fashion.

Milestones will be documented in the profile of the learner and available for review at each competency assessment stage. Sample Evaluation Form


Funding for the fellowship program is based on a combination of clinical hours and internal Warner Slack Fund support. This covers a stipend at the commensurate PGY level, benefits, and operational and educational costs. There are two mechanisms through which we can fund fellows: through our Harvard-wide training grant and through partnerships with clinical departments that allow fellows to continue to keep up their clinical skills and integrate into the environment of the medical center.

NLM Training Grant:

Up to one fellow per year may be awarded a National Library of Medicine Training Grant position, which provides substantial funding for a stipend and pays part way towards a degree in Biomedical informatics through Harvard Medical School. The award covers a portion of the total funding package.

Clinical Work:

Clinical work is not required to fulfill the educational components of the fellowship training program at BIDMC. However, fellows typically work clinically to cover costs associated with the training program. Fellows working clinically are required, like any other fellows, to abide by program policies and ACGME duty hours. 

Fellows typically work in their home clinical department and are jointly onboarded through their home department and the Division of Clinical Informatics, which is part of the Department of Medicine at Beth Israel Deaconess Medical Center. The particular amount of clinical time depends on the clinical duties. As an example, a hospitalist may work 60–70 clinical shifts over the course of a year. 

Patient care, when in service, takes priority over everything else in order to provide outstanding clinical care to all patients. It is the expectation that fellows will continue to work, on average, 40 hours per week doing informatics work as part of the fellowship program. 

Computational Environment

BIDMC Enterprise

Beth Israel Deaconess Medical Center operates enterprise-wide clinical computing systems that support almost every function of an academic medical center. Most of this system is ‘home-grown’ and has been continuously evolving since 1977.  Our electronic health record was first deployed in 1989 and has been implemented in all ambulatory settings (over 70 clinics) and inpatient settings, including critical care, neonatal ICU, and oncology/infusion. In clinical settings, the electronic health record is called webOMR, is a CCHIT-certified system, and qualifies for meaningful use 1 and 2 by providing appropriate services for inpatient and outpatient clinical care.  The system also supports all ancillary departments with either homegrown components or vendor-supplied solutions.

We have internal decision support rules for both inpatient and outpatient care, including medication decision support, renal adjustments, geriatric precautions, and evidence/cost suggestions. In addition, we use vendor-supplied rules for medication prescribing and allergy checking. Our ordering system has support for test selection, and our ambulatory record has reminders and condition- and physiologic-based rules. 

Patient Portal

Additionally, we provide a patient web portal called PatientSite that allows patients to connect with their records (including view, download, and transmit functionality), schedule appointments, and communicate securely with their providers. PatientSite was also created at BIDMC and began serving our patients in 2000.

Fellows and faculty continue to innovate in the area of patient-computer dialogue, with recent projects involving online designation of advance directives, patient-generated health data, and open notes. 

Commercial Vendor EHR

Fellows will also gain experience in commercial vendor EHRs through our community and affiliated hospital centers. These EHRs include Meditech, EPIC, and Cerner.


The fellowship has the following tracks:

  • NIH Research Training Program Track
  • Emergency Medicine Informatics Track
  • Radiology Informatics Track
  • Joint MIT Machine Learning Track

Emergency Medicine Track


The Emergency Medicine Track is a specialized track within the Clinical Informatics Training Program that is designed to create academic leaders in informatics and emergency medicine who will transform practice by analyzing, designing, implementing, and evaluating information systems that improve all aspects of clinical care. Emergency physicians are often called upon to make critical decisions under significant time pressure and with limited information. Well-designed clinical computing systems can ease these pressures and improve the quality and efficiency of emergency care. 


The EM track is only open to candidates who have completed residency in emergency medicine and are board-eligible or board-certified by the American Board of Emergency Medicine.

EM-specific Curriculum

In addition to the core curriculum of the Clinical Informatics training program, fellows in the EM track will supervise EM residents while working clinically in the ED, undertake formal coursework in research methodology, design and evaluate ED-specific clinical applications and undertake mentored research projects. Upon completion of the program, graduates will be prepared to assume a leadership role in academic informatics, leading system development efforts, and conducting independent research.

This training program will help fellows:

  • Become an expert in all stages of the life cycle of clinical information systems, including planning, development, implementation, and support.
  • Develop a thorough understanding of the healthcare environment and how the flow of information can affect clinical care as well as business processes.
  • Develop a comprehensive skillset to design highly usable interfaces and a deep understanding of how this affects clinical users and patient care.
  • Learn how to design, implement, and report the results of a research study.
  • Learn how to develop and write a research grant.
  • Network and establish collaborative relationships with other informaticians on the local and national level.
  • Develop the skills to allow graduates to assume leadership roles at the departmental and hospital levels.

Application Process


Introduction to Fellowship Applications

Physicians who will have completed a primary specialty with an interest in clinical informatics are encouraged to apply to our fellowship program. Formal training in computer science or equivalent self-directed learning is encouraged. Competitive applicants will be familiar with computer science, programming, and the fundamentals of data science and statistics, with the expectation that they will develop skills particular to healthcare data science and evaluation methodology/biostatistics as they proceed through the program. 

Candidates must be ABMS-certified or board-eligible before their expected start date. 

We are unfortunately not able to accommodate other post-doctoral fellows outside of our established informatics training program.

Please familiarize yourself with information about funding (as described above) for the informatics fellowship program prior to applying.

 Application Process:

  • Applicants should apply through ERAS (ACGME ID: 1392414001 ) which opens to applicants in September.
  • Applicants must also submit a Supplemental Application Form
  • BIDMC participates in the Clinical Informatics National Match


  • Sept: ERAS opens to applications
  • Oct -Nov: Fellowship Interviews
  • Dec: National Match Day for Clinical Informatics (instructions will be emailed to applicants)

Late Applicants:

  • All applicants must have been interviewed to be considered for the December match.
  • We leave one spot open for out-of-cycle applicants and will consider applicants for this spot on a rolling basis.