STS-36 was a NASA Space Centre mission, during which Space Shuttle Atlantis carried a classified payload for the U.S. Department of Defence (believed to have been a Misty reconnaissance satellite) into orbit. STS-36 was the 34th shuttle mission overall, the sixth flight for Atlantis, and the fourth night launch of the shuttle program. It launched from Kennedy Space Centre, Florida, on 28 February 1990, and landed on 4 March.

The launch trajectory was unique to this flight, and allowed the mission to reach an orbital inclination of 62°, the deployment orbit of its payload — the normal maximum inclination for a shuttle flight was 57°. This so-called "dog-leg" trajectory saw Atlantis fly downrange on a normal launch azimuth, and then maneuver to a higher launch azimuth once out over the water. Although the maneuver resulted in a reduction of vehicle performance, it was the only way to reach the required deployment orbit from Kennedy Space Center (originally, the flight had been slated to launch from Vandenberg Air Force Base in California, until the shuttle launch facilities there were mothballed in 1989). Flight rules that prohibited overflight of land were suspended, with the trajectory taking the vehicle over or near Cape Hatteras, Cape Cod, and parts of Canada. The payload was considered to be of importance to national security, hence the suspension of normal flight rules.

As a Department of Defense operation, STS-36's payload remains officially classified. STS-36 launched a single satellite, 1990-019B (USA-53), also described as AFP-731. Other objects (1990-019C-G) reportedly appeared in orbit following its deployment.

The mission marked another flight of an 11-pound human skull, which served as the primary element of "Detailed Secondary Objective 469", also known as the In-flight Radiation Dose Distribution (IDRD) experiment. This joint NASA/DoD experiment was designed to examine the penetration of radiation into the human cranium during spaceflight. The female skull was seated in a plastic matrix, representative of tissue, and sliced into ten layers. Hundreds of thermo-luminescent dosimeters were mounted in the skull's layers to record radiation levels at multiple depths. This experiment, which also flew on STS-28 and STS-31, was located in the shuttle's mid-deck lockers on all three flights, recording radiation levels at different orbital inclinations.

Atlantis launched on the STS-36 mission on 28 February 1990 at 2:50:22 EST. The launch was originally set for 22 February 1990, but was postponed repeatedly due to the illness of the crew commander and poor weather conditions. This was the first time since Apollo 13 in 1970 that a crewed space mission was affected by the illness of a crew member. The first rescheduled launch attempt, set for 25 February 1990, was scrubbed due to a range safety computer malfunction. Another attempt, set for 26 February 1990, was scrubbed due to weather conditions. The successful launch on 28 February 1990 was set for a classified launch window, lying within a launch period extending from 00:00 to 04:00 EST. The launch weight for this mission was classified.