The residency program is five years in length. The PGY-1 year is spent in general surgery, preferably completed at University Medical Center. The last four years of training in otolaryngology–head and neck surgery take place at Stony Brook University Medical Center and St. Catherine of Siena Medical Center in nearby Smithtown. All surgical cases and most outpatient encounters have residents in participation. The attending staff supervises the care of all patients.

The outpatient clinics are organized by subspecialty, as follows:

The following is a breakdown of expected areas of participation each year:

This introductory year of general surgery includes a core experience in general, vascular, and neurological surgery, and a full-time rotation in the Surgical Intensive Care Unit. The goal of this year is to become proficient in basic surgical techniques, in the preoperative and postoperative care of patients, in the principles of management of trauma patients, and in intensive care medicine. Residents are expected to learn independent basic skills such as endotracheal intubation, bladder catheterization, and deep venous access through direct supervision.

In this introductory year of otolaryngology–head and neck surgery residency, the goal is to learn the basic science of the specialty, as well as outpatient diagnostic skills, basic surgical techniques in otolaryngology, and the preoperative and postoperative management of head and neck patients.

The first month of this year is a "protected" period with close clinical supervision, including 16 hours of introductory lectures in clinical science and OR emergencies. During the remainder of the year, as in later years, there are formal weekly didactic conferences.

Part of the resident's time is spent in the clinic learning basic diagnostic skills, including the use of flexible and rigid endoscopic equipment and office microscopy. There is "hands-on" teaching in audiology and speech pathology. During daily inpatient rounds, the resident has an intimate knowledge of the clinical status of the patients, assumes increasing responsibility for their management, and learns the essentials of pre- and post-operative management.

The PGY-2 resident also receives an introductory surgical experience to procedures in the head and neck, including tonsillectomy, adenoidectomy, myringotomy and tubes, basic head and neck endoscopy (including introductory use of the laser), and nasal septal surgery. The resident is also responsible for the initial care of trauma patients; simple plastic surgical procedures including excision of skin lesions, skin grafting, and repair of facial defects; tracheostomy, excision of some neck masses, nasal polypectomies, simple sinus procedures, and closed reductions of nasal fractures.

The PGY-3 and PGY-4 years represent a continuum, with an overlap in clinical duties with a progressive increase in independent responsibility. One half of each year is spent at St. Catherine of Siena Medical Center.

In the outpatient setting, the PGY-3 resident participates in the primary care and specialty clinics, and rotates for one month through the allergy/immunology service to gain experience with clinical immunological and rheumatological disorders.

In the operating room, surgical responsibility increases as technical skills are acquired. Surgical cases include pediatric and foreign body endoscopy, laser surgery of laryngeal and pharyngeal lesions, endoscopic sinus surgery, frontal-ethmoidal surgery, frontal sinus osteoplastic flaps, total laryngectomies, myocutaneous flaps, maxillectomy, parotidectomy and thyroidectomy, neck dissection, rhinoplasty, blepharoplasty, facelift surgery, complex facial reconstruction, tympanoplasty with ossicular reconstruction, primary and revision mastoid surgery, stapes surgery, and exploration and excision of middle ear lesions. At St. Catherine of Siena Medical Center, the resident is responsible for day-to-day care of the inpatient and outpatient service, assists in or performs all surgical cases, and prepares monthly head and neck conferences

The surgical experience in PGY-4 is similar to PGY-3, with an increasing role in supervising junior residents. The PGY-4 resident also participates in oral and maxillofacial trauma and plastic post-traumatic and post-ablative and reconstructive procedures. He/she is also principally responsible for coordinating the otolaryngology–head and neck surgery service for half the year at St. Catherine of Siena Medical Center. During clinics at University Medical Center and St. Catherine of Siena, the resident synthesizes information, makes diagnoses, and recommends workup and therapy. A rotation in pathology is planned in which the resident is involved in autopsies, frozen and permanent surgical pathology specimens, and cytopathology.

The chief year is spent integrating clinical diagnostic skills, taking on a more challenging level of surgical experience, and above all, developing the capacity for independent and critical thought and performance. The chief resident is responsible for the administration of the otolaryngology-head and neck service, including on-call schedules, conference schedules and resident staffing of surgical cases. During the six months spent at University Medical Center, the chief resident assumes a more independent role in managing patients in the clinic and operating room. The chief resident supervises the inpatient service.

In the operating room, the chief resident supervises junior residents, and assumes an increasing level of surgical responsibility. The operative experience includes complex head and neck resections, skull base surgery, and neuro-otologic surgery, such as composite resection, maxillectomy, revision stapedectomy, vestibular nerve section, acoustic neuroma resection, cochlear implant surgery, facial plastic and reconstructive surgery of the head and neck, complex or endoscopic and open sinus surgery, pediatric airway reconstruction, and resection of pediatric head and neck tumors.