Launch from the Baikonur Cosmodrome. This flight was the historic mission ISS Expedition One.

Following a two day solo flight Soyuz TM-31 docked with the ISS on November 02, 2000. They activated the life support systems of the station and performed first repairing works. The unloading supplies and equipment from a Progress supply ship (Progress M1-3) was done.

The first four science experiments were started: Protein Crystal Growth - Enhanced Gaseous Nitrogen in the aera of physical sciences and also Middeck Active Control Experiment II (MACE II), Crew Earth Observations (CEO), Space Exposed Experiment Developed for Students (Education-SEEDS. On February 24, 2001 the crew took a short flight of 30 minutes around the ISS to repositioning their Soyuz capsule (Yuri Gidzenko at the controls) from the docking port of the Zvezda module to the docking port of the Zarya module.

The plasma crystal experiment, known as PKE-Nefedov, was one of the first natural science experiments conducted on the space station. It was a collaboration between the Max Planck Institute for Extraterrestrial Physics in Germany, and the Institute for High Energy Densities (part of the Russian Academy of Sciences).

An example of a low-maintenance experiment was the protein crystal growth experiment, which had also been flown on previous shuttle missions. The goal was to produce better protein crystallizations than those produced on the Earth, and hence allowing for a more accurate model of protein structures. Of the 23 proteins and viruses attempted during Expedition 1, only four resulted in successful crystallizations, which was a lower success rate than predicted. Of those successful was the low-calorie sweetener Thaumatin, whose crystals diffracted at a higher resolution than Earth-grown crystal, which resulted in a more accurate protein structure model.

Another research activity was measuring the crew's heart rates and the station's carbon dioxide levels to determine the effect of exercise on the station.

During her stay on board of the ISS the crew of expedition 1 carried out the following scientific experiments:
ARISS (Amateur Radio on the International Space Station),
Brados (Acquisition of Data About the Radiological, Electromagnetic and Different Physical Environments on Board ISS, and Their Effects on the Safety of the Crew, Space Equipment and Materials),
Cardio-ODNT (Dynamics of the Main Factors of Cardiac Function, of Central and Regional Circulation in Rest and During the Influence of Lower Body Negative Pressure),
CEO (Crew Earth Observations),
Clinical Nutrition Assessment (Clinical Nutrition Assessment of ISS Astronauts, SMO-016E),
Education-SEEDS (Space Exposed Experiment Developed for Students),
Environmental Monitoring (Environmental Monitoring of the International Space Station),
Identifikatsia (Identification of the Sources of Dynamic Loads on ISS),
Inflight Education Downlinks (International Space Station Inflight Education Downlinks),
Iskazheniye (Determination and Analysis of Magnetic Interference on ISS),
ISS Acoustics (International Space Station Acoustic Measurement Program),
Izgib (Effect of Performance of Flight and Science Activities on the Function of On-Orbit Systems on ISS (Mathematical Model)),
Latent Virus (Incidence of Latent Virus Shedding During Space Flight),
MACE-II (Middeck Active Control Experiment-II),
Paradont (Condition of Peridontal Tissues in Space Flight),
PCG-EGN (Protein Crystal Growth-Enhanced Gaseous Nitrogen Dewar),
Plasma Crystal (Dusty and Liquid Plasma Crystals in Conditions of Microgravity),
Privyazka (Development of High Precision Orientation of Scientific Devices in Space with Reports of Deformation of the ISS Hull),
Prognoz (Development of a Method of Operational Prediction of Work Load on Crew Piloting Objectives),
Sprut-MBI (Determination of Intracellular and Extracellular Fluid Volume in Humans in Space Flight),
Tenzor (Definition of Dynamic Characteristics of ISS),
Uragan (Hurricane: Experimental Development of Groundbased System of Monitoring and Predicting the Progression of a Naturally Occurring Technogenic Catastrophe).

Common work with the visiting crews of STS-97 (December 02, - December 09, 2000) and STS-98 (February 09, - February 16, 2001) was done.

The crew returned to Earth with STS-102.