Launch from the Baikonur Cosmodrome; landing 405 km west of Arkalyk.

In the spring of 2001, a taxi mission to the space station was being scheduled to take place on October 2002. At first the crew was to be Commander Sergei Zalyotin and Flight Engineer Frank De Winne. However, a report released on February 2002 stated that American musician Lance Bass was interested in joining the crew for a one-week mission on board the Russian spacecraft. The mission began to fall through, and by September 2002 they had discontinued the training of Lance Bass due to the mission organizers' failure to meet the terms of the contract. They filled the vacant seat left by Lance Bass with Russian cosmonaut Yuri Lonchakov.

Soyuz TMA-1 became the fourth taxi crew to the ISS. Following a two day solo flight Soyuz TMA-1 docked to ISS on November 01, 2002 and common scientific work with expedition 5 was performed. Frank De Winne worked as part of the ESA program Odissea.

The ISS' escape craft (Soyuz TM-34) was replaced; Soyuz TMA-1 served as a new lifeboat.

While the Soyuz TMA-1 was on orbit, the Feb 2003 Columbia shuttle accident occurred and required a change in crew changeout process. The Soyuz system would now be the sole method for crew to launch to and return from ISS, until the space shuttle was returned to service in July 2005.

Soyuz TMA-1 disembarked from ISS on May 4, 2003 and immediately began its return to Earth, marking the first entry and descent for this Soyuz class. A technical malfunction caused the Soyuz control system to abandon the gentler controlled entry and descent and instead fall back to the harsher ballistic reentry and descent. This resulted in a steep and off target landing of the spacecraft. The craft landed 300 miles short of the planned area, and the crew was subjected to severe gravitational loads. Communication with the Soyuz was lost because one antenna was ripped off during descent, and two more did not deploy. The crew regained communications through an emergency transmitter after landing. Due to this event, future crews would be provided with a satellite phone at their disposal to establish contact with recovery forces.

Subsequent Soyuz TMA missions were able to successfully execute controlled reentries, until the Soyuz TMA-10 and Soyuz TMA-11 missions which both also reverted to ballistic descents.