Virenque, the 30-year-old Moroccan-born son of a French army officer, appeared along with five former members of the Festina training staff - including then sports director Bruno Roussel and Willy Voet, the team masseur.
The defendants, who include French racing star Richard Virenque, have been charged with various offences connected with encouraging and facilitating the use of illegal drugs in sporting competitions.
The trial follows nearly two years of accusations and counter-accusations in France over drug-taking among professional cyclists.
The Tour de France scandal became known as the 'Festina Affair' after the Andorran-registered watchmaking company which sponsored the team taking part in the race in 1998.
Virenque, the 30-year-old Moroccan-born son of a French army officer, appeared along with five former members of the Festina training staff - including then sports director Bruno Roussel and Willy Voet, the team masseur.
Chemist Christine Paranier and her husband Eric, who are accused of supplying Festina with illegal products, were also in court.
Festina's masseur was stopped on the Franco-Belgian border on his way to the race in possession of a range of prohibited substances, triggering a massive investigation.
The entire team was kicked out of the Tour after 40 bottles of doping products, mainly the stamina-boosting hormone erythropoietin (EPO), were found in the team car, while the race itself was almost abandoned.
French Cycling Federation president Daniel Baal said the trial was necessary but questioned whether it would do anything to eradicate doping from cycling.
"On the basic issue, and that is the scourge of doping, the trial won't serve any purpose," Baal conceded.
"The dopers are stronger than those who combat them," he said, adding that "doping is widely used in high-level sport."
The trial is expected to last until 10 November.