Launch from Cape Canaveral (KSC) after two delayed launches due of technical problems (abort on July 20, 1999) and bad weather (on July 22, 1999). Landing on Cape Canaveral (KSC).

Columbia did not reach the planned orbit. Five seconds after liftoff, an electrical short disabled one primary and one secondary controller on two of the three main engines. In this event, the engines automatically switched to their backup controllers. The short was later discovered to have been caused by poorly routed wiring which had rubbed on an exposed screw head. This wiring issue led to a program-wide inspection of the wiring in all orbiters. Concurrently, an oxidizer post, which had been intentionally plugged, came loose inside one of the main engine's main injector and impacted the engine nozzle inner surface rupturing a hydrogen cooling line allowing a small leak. Because of the leak, the engine's controller saw an increase in use rate of hydrogen. The controller assumed the extra hydrogen was being burned in the engine (rather than being leaked overboard as it actually was) and increased the oxidizer flow to maintain the presumptive mixture ratio, resulting in a premature engine shutdown near the end of the projected burn due to low liquid oxygen level. Despite the premature shutdown, the vehicle safely achieved a slightly lower orbit and was able to complete the mission as planned. This incident brought on a maintenance practice change which required damaged oxidizer posts to be removed and replaced as opposed to being intentionally plugged, as was the practice beforehand.

Eileen Collins became the first female Shuttle commander. .

The X-Ray-telescope CHANDRA was deployed on flight day one. CHANDRA was the most sophisticated X-ray observatory ever built. It is designed to observe X-rays from high energy regions of the universe, such as hot gas in the remnants of exploded stars.

Other payloads on STS-93 included the Midcourse Space Experiment (MSX), the Shuttle Ionospheric Modification with Pulsed Local Exhaust (SIMPLEX), the Southwest Ultraviolet Imaging System (SWUIS), the Gelation of Sols: Applied Microgravity Research (GOSAMR) experiment, the Space Tissue Loss – B (STL-B) experiment, a Light Weight Flexible Solar Array Hinge (LFSAH), the Cell Culture Module (CCM), the Shuttle Amateur Radio Experiment – II (SAREX – II), EarthKAM, Plant Growth Investigations in Microgravity (PGIM), the Commercial Generic Bioprocessing Apparatus (CGBA), the Micro-Electrical Mechanical System (MEMS), and the Biological Research in Canisters (BRIC).

The Southwest Ultraviolet Imaging system (SWUIS) was based around a Maksutov-design ultraviolet (UV) telescope and a UV-sensitive, image-intensified Charge-Coupled Device (CCD) camera that frames at video frame rates. Scientists can obtain sensitive photometric measurements of astronomical targets.

The Shuttle Ionespheric Modification with Pulsed Local Exhaust (SIMPLEX) payload activity researched the source of Very High Frequency (VHF) radar echoes caused by the orbiter and its OMS engine firings. The Principal Investigator (PI) used the collected data to examine the effects of orbital kinetic energy on ionospheric irregularities and to understand the processes that take place with the venting of exhaust materials.

The Shuttle Amateur Radio Experiment (SAREX-II) demonstrated the feasibility of amateur short-wave radio contacts between the shuttle and ground-based amateur radio operators. SAREX also served as an educational opportunity for schools around the world to learn about space by speaking directly to astronauts aboard the shuttle via amateur radio.

The EarthKAM payload conducted Earth observations using the Electronic Still Camera (ESC) installed in the overhead starboard window of the Aft Flight Deck.

The Plant Growth Investigations in Microgravity (PGIM) payload experiment used plants to monitor the space flight environment for stressful conditions that affect plant growth. Because plants cannot move away from stressful conditions, they have developed mechanisms that monitor their environment and direct effective physiological responses to harmful conditions.

The Commercial Generic Bioprocessing Apparatus (CGBA) payload hardware allows for sample processing and stowage functions. The Generic Bioprocessing Apparatus – Isothermal Containment Module (GBA-ICM) is temperature controlled to maintain a preset temperature environment, controls the activation and termination of the experiment samples, and provides an interface for crew interaction, control and data transfer.

The Micro-Electrical Mechanical System (MEMS) payload examines the performance, under launch, microgravity, and reentry conditions of a suite of MEMS devices. These devices include accelerometers, gyroscopes, and environmental and chemical sensors. The MEMS payload is self-contained and requires activation and deactivation only.

The Biological Research in Canisters (BRIC) payload was designed to investigate the effects of space flight on small arthropod animals and plant specimens. The flight crew was available at regular intervals to monitor and control payload/experiment operations.