In addition to residency training, there are six clinical fellowships at MEEI: Neurotology, Head and Neck Surgery, Thyroid Surgery, Laryngology, Rhinology, and Pediatric Otolaryngology, and three clinical fellowships in Pediatric Otolaryngology at Children's Hospital. At any one time, there are approximately 20 research fellows and pre- and postdoctoral students.

The Infirmary is a major teaching site for the Ph.D. Speech and Hearing Bioscience and Technology (SHBT) Program sponsored by the HST Program of the Massachusetts Institute of Technology and the Harvard Medical School.