STS-39 was originally a classified Department of Defense mission. However, after the completion of the mission, information regarding the payloads carried was released. The primary payloads on this mission were the Air Force Program-675 (AFP-675) and the Infrared Background Signature Survey (IBSS). The AFP-675 was a unique demonstration of the ability to command, control, and evaluate a system of experiments without ground commands or telemetry data. The experiments will be measuring infrared, ultraviolet, visible, and X-ray emissions. The IBSS consisted of the Critical Ionization Velocity Experiment, the Chemical Release Observation, and the Shuttle Pallet Satellite-II (SPAS-II) experiments. IBSS collected infrared, ultraviolet, and visible measurements of natural and induced geographical phenomena.
Life Sciences experiments on this mission included multiple Detailed Supplementary Objectives (DSOs). A DSO is a NASA-sponsored investigation performed by Space Shuttle crewmembers, who serve as the test subjects. These studies required minimal crew time, power and stowage. Biomedical DSOs focus on operational concerns, including space motion sickness, cardiovascular deconditioning, muscle loss, changes in coordination and balance strategies, radiation exposure, pharmacokinetics and changes in the body's biochemistry.
Other payloads on this mission included the Space Test Payload-1, the Multi-Purpose Release Canister, Radiation Monitoring Equipment III and Cloud Logic to Optimize Use of Defense Systems (CLOUDS-I).
The landing of the Shuttle Discovery was originally planned at Edwards Air Force Base in California, but was diverted to Kennedy Space Center due to unacceptably high winds. The Space Shuttle touched down at KSC on May 6, 1991.