Rufus Cole, the Hospital's first director, was a major architect of clinical science. He set the permanent course of the Hospital as an independent, central unit of the Rockefeller Institute. Thus, from its opening in 1910, the Hospital was completely equipped to conduct its own research programs. This permitted physicians to engage in fundamental studies in Hospital laboratories on the disease problems they dealt with on the wards of the Hospital. Cole also intended that research from the Hospital would eventually "play its part in the reorganization of medical teaching in this country." A new kind of scientist emerged from this pioneering model of the research Hospital: the clinical investigator who serves as a link between the practicing physician and the basic scientist.

By 1940, nearly half of the major positions in academic internal medicine in the United States were filled by Hospital alumni trained in clinical investigation. Among the many important scientists associated with the Rockefeller Hospital are Oswald Avery, Colin MacLeod and Maclyn McCarty, who established that DNA is the genetic material; Louise Pearce, Simon Flexner, Wade Hampton Brown, Walter Jacobs, and Michael Heidelberger, who developed the first widely used drug, tryparsimide to treat trypanosomiasis (sleeping sickness); Donald Van Slyke, father of clinical chemistry; Rene Dubos, whose work led to the first rationally developed antibiotic; Rebecca Lancefield, who developed a classification system of the streptococci; Henry Kunkel, a founder of clinical immunology; and Vincent P. Dole, Marie Nyswander and Mary Jeanne Kreek, who inaugurated methadone treatment of heroin addiction.

Over the Hospital's history, interactions between clinical and nonclinical scientists have taken many productive forms that have greatly advanced the life sciences. Some other major contributions include the development of the oxygen chamber, influenza immunization, blood chemistry analysis using the Van Slyke manometric apparatus, methods for blood transfusion and blood storage, diagnostic tests for lead poisoning, new therapies for psoriasis, and multiple drug therapy of HIV infection, as well as the detailed characterization of numerous diseases including poliomyelitis, Wilson's disease, and porphyria.

Until 1963, the Hospital, which currently consists of a 20 bed inpatient facility and the Robert & Harriet Heilbrunn Outpatient Research Center, was supported entirely by institutional funds. From 1963 until 2006 it was funded by both Rockefeller University and the General Clinical Research Center (GCRC) Program of the National Institutes of Health (NIH). In September 2006, the University was awarded a Clinical and Translational Science Award (CTSA) from the NIH National Center for Research Resources. The award, the successor to the GCRC Program, led to the establishment of the Rockefeller University Center for Clinical and Translational Science, and provided additional resources to complement those coming from the University for the support of the University's human subjects research.