Clinical microbiology fellow pipetting in the lab

Graduate medical education in laboratory medicine and pathology at Mayo Clinic

Page Content


The Clinical Microbiology, M.D. (ACGME) or Ph.D. (CPEP) Postgraduate Fellowship at Mayo Clinic's campus in Rochester, Minnesota, offers an outstanding educational experience for you to develop your expertise in medical microbiology within the integrated Mayo Clinic system, renowned for quality medical care and health care innovation. Learn more about the program and what fellows can expect by watching this 5 minute program overview video.

This fellowship develops your knowledge and skills in diagnostic microbiology, infectious disease pathology, clinical consultation related to microbiology and infectious diseases, and clinical laboratory management.

Upon completion of this fellowship, you will be equipped with the skills necessary for a successful career as a director of a clinical microbiology laboratory that diagnoses infections caused by bacteria, fungi, mycobacteria, parasites, and viruses. 

Mayo Clinic's campus in Rochester, Minnesota, offers two clinical microbiology fellowship programs:

  • Ph.D. program (CPEP). The CPEP program is a two-year program designed for individuals with a doctoral degree who want specific training in clinical microbiology.
  • M.D. program (ACGME). The ACGME program is a one-year program for individuals with a medical degree and previous residency training in the U.S. or Canada in pathology or an infectious diseases fellowship.

Unique program opportunities include:

  • Comprehensive training and hands-on experience in all areas of clinical microbiology provided through rotations in seven specialized clinical microbiology laboratories and daily interactions with eight board-certified microbiology medical lab directors
  • A strong clinical component, which includes on-call responsibilities and interacting with infectious disease clinicians and other clinical services involved in patient care
  • A unique dual practice with both an in-house hospital practice and a large reference laboratory service
  • Opportunity to experience different clinical microbiology laboratory settings, with rotations at the Mayo Clinic campus in either Jacksonville, Florida, or Scottsdale, Arizona
  • Training opportunities to observe and perform diagnostic testing methods ranging from classic reference assays, such as bacterial biochemical analysis, viral culture, complement fixation and immunodiffusion, to contemporary molecular assays, cutting-edge next generation sequencing technology, digital imaging, and artificial intelligence (AI) algorithms
  • Exposure to state-of-the-art anti-microbial susceptibility testing methods
  • Specific training in infectious disease pathology (diagnosis of microorganisms in histopathology and cytopathology preparations)
  • Research opportunities in test development including molecular applications, next generation sequencing, and digital pathology/AI with the potential to publish and present at national meetings
  • All fellows publish at least one article in a peer-reviewed journal and nearly all fellows present a poster or speak at a regional or national conference

hospital in Minnesota and nationally recognized on the Best Hospitals Honor Roll (U.S. News, 2023-2024)

Video: Program Overview


Video: Program Overview

Video: A Day Above Mayo Clinic


Video: A Day Above Mayo Clinic

Clinical Microbiology fellow prepping culture specimens in the lab at Mayo Clinic in Rochester, MN.

Your training experience

As a fellow at Mayo Clinic, you'll have access to robust clinical, educational, and research resources. You'll find support both inside and outside of the campus to promote physical and mental wellness and ensure your work/life balance.

Bobbi Pritt, M.D. and Ellie Theel, Ph.D.

Director's welcome

Our curriculum integrates didactic sessions and hands-on training at the bench, alongside self-directed learning and research time, all designed to provide you with the necessary skills and knowledge you will need to become a leader in the field of clinical microbiology.


The CPEP program is accredited by the Committee on Postgraduate Educational Programs (CPEP) of the American Society for Microbiology (ASM) and meets the certification requirements for the American Board of Medical Microbiology (ABMM).

The ACGME program is accredited by the Accreditation Council for Graduate Medical Education (ACGME) and meets the certification requirements of the American Board of Pathology (in Medical Microbiology).


When you successfully complete Mayo Clinic's Clinical Microbiology CPEP Postgraduate Fellowship (including the experience requirement), you will be eligible for certification by the American Board of Medical Microbiology (ABMM)

When you successfully complete Mayo Clinic's Clinical Microbiology ACGME Postgraduate Fellowship, you will be eligible for certification by the American Board of Medical Microbiology (ABMM) and the American Board of Pathology (in Medical Microbiology).

Program history

The Division of Clinical Microbiology at Mayo Clinic has been training fellows since 1914. Since that time, more than 150 fellows have completed training.

The CPEP program received accreditation in 1972 and the ACGME program received accreditation in 1992. Fun fact: The Clinical Microbiology CPEP Postgraduate Fellowship at Mayo Clinic was the second in the country to receive accreditation (the first was the University of Washington in 1964).

More from Mayo Clinic School of Graduate Medical Education

Mayo Clinic resident checking heartbeat of teen patient

Choosing Mayo Clinic

Mayo Clinic campus in Rochester, Minnesota.
Campus and community

Rochester, MN

Group of consultant, nurse, and residents discussing case in hallway at Mayo Clinic.

Stipend and benefits