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Section of Gastroenterology

Houston, Texas

The Alkek Building at Baylor College of Medicine
Gastroenterology and Hepatology Section
not shown on screen


The Section of Gastroenterology & Hepatology at Baylor College of Medicine offers a fellowship program in Gastroenterology and Hepatology that accepts up to five new fellows each year beginning in July. The goal of this program is to prepare individuals for academic careers by broad training in gastroenterology and hepatology.

Our program is nationally recognized and highly competitive; each year we receive an average of 350 applications. Our faculty serve at the highest levels of many national organizations, including the American Gastroenterological Association, the American College of Gastroenterology, American Association for the Study of Liver Disease and the Crohn's and Colitis Foundation of America. Several faculty are elected members to the American Society for Clinical Investigators.

Academic Clinical Track

The clinical track is a three-year program for fellows who intend to enter clinical academic practice upon completion of the training program. The emphasis is on clinical gastroenterology and hepatology with the opportunity for more formal clinical research training.

The fellowship program is based at several hospitals and clinics, including the Michael E. DeBakey Veterans Affairs Medical Center Ben Taub Hospital, St. Luke’s Episcopal Hospital, the Baylor Clinic, the Houston Hospital for Specialized Surgery, and The Methodist’s Hospital.

These training sites provide a diverse experience in different clinical environments.

First year fellows spend approximately half their time at the MEDVAMC and the other half at BTH on a general GI services. Second year fellows divide their time among the following rotations: SLEH; hepatology; research; and general GI. The third year allows the fellows to develop sub-sub specialty expertise and hone their ability to function as a consultant.

Focused rotations are available in hepatology, IBD, motility and endoscopic ultrasound. During the second and third year, fellows are exposed to ERCP, but this experience is not designed to train to proficiency. During all three years, fellows will have a weekly continuity clinic at BTGH.

Research Track

We offer research training in Digestive Disease Epidemiology and Outcomes.

For applicants for July 2013 starting date, the research track is a comprehensive four-year program for those who plan to pursue a research career. The research track will include 24 months of clinical rotations. All fellows must complete a minimum of 18 months of clinical gastroenterology training to be permitted to sit for the GI board exam. The other two years will include graduate school work, mentored research and career development activities.

Funding for the research track fellowship is primarily from Institutional Public Health Service fellowships. Salaries from federal sources carry a year-for-year payback that requires the fellow to work in an academic setting after completion of training. Because of these funding considerations, applicants to our research programs must be either US citizens (by birth or naturalization) or hold a permanent immigrant visa status (green card).

Salary is commensurate with cumulative experience. Research fellows on training grants are paid according to the current NIH pay scale. Please refer to the NIH notice in regard to stipends. Stipend amount is determined by the number of previous years of related work experience, including lab time, private sector time, hospitalist time, and time as Chief Resident.

Advanced Endoscopy Fellowship

The Baylor Advanced Endoscopy fellowship is a one year program that provides mentored career development in advanced diagnostic and therapeutic endoscopy. The trainee will receive advanced endoscopic training in both the cognitive and procedural aspects of advanced endoscopic procedures with the goal of being trained as an academic interventionalist. The trainee will be expected to partake in active research projects and initiate their own projects. Most of the advanced training will revolve around ERCP and EUS. The trainee will also get exposure to luminal stenting, endoscopic mucosal resection, radiofrequency ablation, confocal endomicroscopy, and other complex procedures. For more details please contact the advanced endoscopy director: Yasser Shaib, M.D., M.P.H. (

Liver Transplant Fellowship

We have an ACGME approved one-year liver transplant fellowship. We accept up to three fellows per year. Applicants must have completed or expect to complete a three-year gastroenterology fellowship training. For more details please contact the liver transplant fellowship director, John Vierling, M.D. (

Visiting Students/Residents

Medical students from United States and international programs may rotate through GI electives by applying the Baylor Office of Student Affairs. Neither United States nor international residents are permitted. There are no observerships at Baylor.

Fellowship Training Highlights

The GI Section is active in several clinical venues:

The MEDVAMC has a faculty of 11 gastroenterologists and hepatologists. There is an active inpatient GI as well as a separate inpatient hepatology consult service that follow 15-20 patients on average per day. The GI Endoscopy Center at MEDVAMC consists of 3 endoscopy rooms and performs an average of 8,000 procedures annually.

The GI service at BTGH has a faculty of 5 gastroenterologists. The endoscopy center consists of 4 endoscopy rooms and performs approximately 5000 procedures annually, both on in patients and outpatients. The fellows’ continuity clinic is at BT and provides exposure to a wide variety of clinical conditions in both gastroenterology and hepatology.

Baylor Clinic practice involves a busy referral practice. Patients are referred by local physicians and community gastroenterologists from inside and outside Houston. Additionally in patients are seen at St. Luke’s Episcopal Hospital and Methodist hospitals. The faculty perform about 3000 procedures annually.

Specific areas of clinical expertise in the section include:

  • Motility:Our Gastrointestinal Motility laboratories at MEDVAMC and SLEH offer high resolution esophageal manometry, Bravo wireless pH monitoring, and impedance-pH monitoring. Our Motility laboratories perform an average of 300 procedures per year. The fellows have an opportunity to observe and aid in the performance of these procedures, and they receive instruction on their interpretation. In addition, during a dedicated luminal rotation, they have an opportunity to see patients in the MEDVAMC and Baylor motility clinic, where they are exposed to patients with GI motility issues.
  • Inflammatory Bowel Disease: Three faculty members have a focused practice in IBD providing tertiary referral care, clinical trials, and an active clinical research program.
  • Transplant Hepatology: The Transplant Hepatology group is comprised of six faculty. There is an active transplant program with > 100 liver transplants annually. Additionally there is an extremely busy clinical trials program focused on viral hepatitis, and other liver diseases.
  • Advanced Endoscopy: There is an active advanced endoscopy group of seven gastroenterologists spanning the Baylor hospitals providing ERCP/EUS and other innovative endoscopic procedures.

Conferences and Seminars

There are a number of formal and informal clinical and research teaching activities within the division:

  • GI Grand Rounds
  • Topic Oriented Didactic Conference
  • Monday Conference (Rotating Endoscopy, Pathology, Motility, Liver Journal Club)
  • Thursday Conference (Rotating GI Mortality & Morbidity, Research, Nutrition, Professor’s Lecture, Practice Management)
  • Journal Club
  • Multidisciplinary IBD Conference

All fellows regardless of track are required to attend a composite of 85 percent of the educational conferences.


Each clinical fellow has one half-day per week of continuity clinic. In this clinic, fellows see 4-5 new patients and 4-5 return patients. This clinic is precepted by several GI attendings. In addition, fellows participate in the following subspecialty clinics: general liver clinic, IBD clinic, and motility clinic/lab.


For fellows in the Academic Clinical Track, it is expected that at the end of the first year a project mentor will be chosen and the outline of a research project will be developed. The mentor will help identify the resources required to carry out the research project. During the second year the fellow is expected to carry out the research project and during the third year continue further work on the project or a new project and write the project up for publication. It is expected that preliminary work from the research project will be submitted in abstract form either to the AGA, ACG, or AASLD.

Typical Rotations on the Academic Clinical Track:

  • Year 1: 5 months MEDVAMC, 6 months BTGH, 1 month SLEH
  • Year 2: 3 months Hepatology, 3 months Research, 3 months SLEH, 3 months BTGH/MEDVAMC
  • Year 3: 3 months Luminal Service (Motility/IBD); 3 months SLEH (Advanced Endoscopy); 6 months Senior Fellow BTGH/MEDVAMC (or Sub-sub specialty track)

    (MEDVAMC: Michael E. Debakey VA Medical Center; BTH: Ben Taub Hospital; SLEH: St. Luke's Episcopal Hospital)

Current Fellows

For a listing of our current fellows, please go to Gastroenterology Fellows.

Applying for Academic Clinical Track

Applicants to both the clinical and research fellowship track positions must have completed an internal medicine residency program from an accredited US institution. For the clinical track, Baylor College of Medicine accepts applicants who have been issued a J-1 visa and who hold a current ECFMG certificate.

At the time of application, foreign nationals must hold a J-1 visa. We do not accept conditional guarantees that the individual may or may not have a J-1 visa prior to or at the time of fellowship.
However, Baylor College of Medicine does not sponsor E-B or O-1 visas, including EAD (Employment Authorization Document). M.D. fellows elect either a clinical or research academic track.

Fellows are paid in accordance with the GME pay scale because, as subspecialty residents, they are appointed through our Graduate Medical Education Office.

Applying for GI Research Fellowship Track

Who should apply?

Applicants for this track should be seriously interested in spending two intense years learning epidemiology, biostatistics, evidence-based medicine, outcomes research, and health services research. This two-year research-training program is funded by the NIH.

Candidates should be motivated, and eager for a challenging program in an important area of GI research. Women and minorities are encouraged to apply. If this research fellowship is funded by a grant from the National Institutes of Health, fellows must be U.S. citizens or permanent residents (no EAD). Stipends are in accordance with the NIH scale depending on years of previous related experience.

How many slots are available?

Each year we offer one position. For 2013 we anticipate one available slot.

The Gastroenterology Match

We will be participating in the GI Match for positions beginning July 1, 2013. The AGA has made available on its web site a list of programs participating in the Match. The listing is featured on the Education and Training section of Questions or comments can be directed to The National Residency Match Program website for detailed information on how the Match program works, phone 202-862-6077 or 1-866-617-5834.

For 2013, we have again decided to participate in the Electronic Residency Application Service. To learn how to apply, how the process works, and those GI programs participating in this process, please visit, phone 202-828-0508.

We require - through ERAS - the following application materials: application, resume, personal statement, USMLE test scores steps I and II, transcript, and three letters of recommendation.

Our program offers two fellowship tracks: one clinical (academic clinician), and one research track (digestive disease epidemiology and outcomes). Both tracks are listed for participation in the Match program. Clinical is our traditional three-year clinical program. The research track requires two years of MPH/MS work and two years of clinical work. All tracks prepare fellows for eligibility to sit for GI board exams. You may designate whichever track(s) are of interest to you. However, please note that if you choose more than one track, your application will be considered for only one track for interview and will be routed to that particular review committee.

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