Launch from Cape Canaveral (KSC); landing on Edwards AFB. Originally the launch was planned for November 03, 1994. Due to bad weather at the emergency landing places in Portugal, Spain and Morocco the launch was delayed.

STS-66 carried out the mission "ATLAS-3". It continued the series of Spacelab flights to study the energy of the sun and how it affects the Earth's climate and environment. ATLAS means Atmospheric Laboratory for Applications and Sciences. The ATLAS-03 mission made the first detailed measurements from the Shuttle of the Northern Hemisphere's middle atmosphere in late fall. The timing of the flight, when the Antarctic ozone hole is diminishing, allowed scientists to study possible effects of the ozone hole on mid-latitudes, the way Antarctic air recovers, and how the northern atmosphere changes as the winter season approaches.

The crew of the Atlantis deployed the CRISTA-SPAS platform and retrieved it after a freeflight of of more than eight days. It was mounted on the Shuttle Pallet Satellite, the payload was designed to explore the variability of the atmosphere and provide measurements that will complement those obtained by the Upper Atmosphere Research Satellite launched aboard Discovery in 1991. CRISTA (Cryogenic Infrared Spectrometer Telescope for Atmosphere) instrument gathered first global information about medium and small scale disturbances in trace gases in middle atmosphere, which could lead to better models of the atmosphere and Earth's energy balance. CRISTA-SPAS was a joint U.S./German experiment. Experiments in the areas of solar and atmospheric physics were done. For retrieval of CRISTA-SPAS, a different approach method to the spacecraft was successfully tested as prelude to upcoming U.S. Shuttle/Russian Space Station MIR docking flights. Called R-Bar approach, it is expected to save propellant while reducing risk of contamination to Mir systems from orbiter thruster jet firings

Due to high winds and rain showers at Cape Canaveral STS-66 was diverted to the Edwards AFB.