The Australian second seed dismissed the American Steve Campbell 6-2, 6-2 in just over an hour and demonstrated the form he will need to contest the world No 1 ranking for the year's end.
Last year in Lyons, Rafter lost in the first round and handed back to the organisers the cheque he had been offered to enter the tournament.
"I gave it back because I felt I was not well prepared enough for this tournament. Had I won a match it would have been different of course," he said.
This time Rafter has not experienced the sort of comedown he suffered after winning the US Open crown for the first time last year. Having retained that title, he is still theoretically capable of preventing the American Pete Sampras from finishing the season in top place once again.
Rafter, Sampras and the Chilean Marcelo Rios, who briefly took the No 1 ranking from Sampras earlier this year, are the only players with a reasonable chance of topping the rankings at the end of the year.
All three are playing in Lyons, with Sampras and Rios entering the tournament today, but none has ranking points to lose.
The defending champion and No 8 seed, Fabrice Santoro of France, was in good form yesterday as he beat his countryman, Stephane Huet, 6-3, 6-3.
In Ostrava Slovakia's Jan Kroslak upset the fifth-seeded Croatian Goran Ivanisevic 4-6, 6-2, 7-6 and David Prinosil, of Germany, defeated the sixth seed, Mark Philippoussis of Australia, 6-3, 6-7, 6-3 in the Czech Indoor tournament.
On a day of surprises, the most astonishing defeat came in the women's event, the Kremlin Cup in Moscow, where the 16-year-old Russian, Nadezhda Petrova, ranked 175 in the world, beat the world No 20 and former French Open champion, Iva Majoli, 6-7, 7-6, 6-0 in the first round.