While similar to other elite medical schools, Weill Cornell is different in some important respects. Problem-based learning is emphasized more thoroughly than at perhaps any other school. Cornell recruits the highest percentage of underrepresented minorities of any non-minority medical school. Over half of the medical students do international clinical rotations. The Tri-Institutional MD-PhD Program relies upon not only the faculty and resources of Cornell but on Memorial Sloan-Kettering Cancer Center and Rockefeller University, both of which lie adjacent to the Cornell campus.

Weill-Cornell's administrative connections are complex. Its teaching hospital is Weill Cornell Medical Center, which along with the Columbia University Medical Center, comprises the New York-Presbyterian Hospital. Unlike many similar efforts, the New York Hospital-Columbia Presbyterian Hospital merger has not only led to the reduction of administrative redundancy but has strengthened academic programs on both campuses.

In addition to its affiliations with NYPH, MSKCC, and Rockefeller, Weill Cornell is the academic center for the Hospital for Special Surgery, which lies across the street and the The Methodist Hospital in Houston, a hospital which had been — until 2004 — the primary private teaching hospital for Baylor College of Medicine.

Cornell has also opened the first American medical school to be located outside of U.S. borders. The Weill Cornell Medical College in Qatar opened for instruction in 2004. Its facilities are found in Education City, Qatar near Doha. The Qatar campus offers a six-year integrated medical education program primarily focused on patient care.

The hospital is a member of the Planetree Alliance, a nonprofit association of health-care institutions set up to promote practices to make patients less intimidated and more comfortable with the health care they receive.