Its primary mission was to launch the Chandra X-ray Observatory, the heaviest payload ever carried by the Space Shuttle system, at 22,780 kilograms (50,222 lb).

This anomalous event and the automatic response to the leak by the right engine's controller did not violate any launch commit criteria and liftoff proceeded normally.

The hydrogen leak and increased oxidizer consumption resulted in the right engine deviating from the desired oxygen/hydrogen mixing ratio of 6.03 and running hotter than normal.

The increased oxidizer consumption during ascent resulted in a premature shutdown of all three engines near the end of the projected burn due to low liquid-oxygen level sensed in the External Tank.

Though the premature shutdown resulted in a velocity 15 ft/s (4.6 m/s) lower than targeted,[11] the vehicle safely achieved its intended orbit and completed the mission as planned.

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 mass 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 Shuttle Ionospheric 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.

In particular, the purpose was to demonstrate that composite ceramic precursors composed of large particulates and small colloidal sols can be produced in space with more structural uniformity.

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 Biological Research in Canisters (BRIC) payload was designed to investigate the effects of space flight on small arthropod animals and plant specimens.

In 2007, the Mint announced it would for the first time publicly display the 12 space-flown gold dollars at the American Numismatic Association's World's Fair of Money in Milwaukee, Wisconsin.