Operating rooms in the days before electric light were typically on the top floor of a hospital building to maximize the availability of natural light. When the hospital first opened, it was lit with whale oil lamps, which were not enough to provide good light for surgery. This skylight is inside a dome-shaped roof, a common feature of architecture for important buildings designed in the Federal style. The architect, Charles Bulfinch, was a leader in this style.

It is sometimes said that the top floor was also chosen for the operating room because it was furthest away from the wards, because the hospital was constructed before anesthesia and the sounds of patients undergoing surgery might disturb other patients.