Apparently there is evidence that Armstrong doped during his first Tour de France victory:
In six urine samples taken from Armstrong during the 1999 Tour de France, doping researchers found EPO in tests conducted for scientific purposes five years later. Dr. Jacques de Ceaurriz, the director of the laboratory that conducted these tests, confirmed on Tuesday a corresponding report in the Tuesday edition of the sports newspaper L'Equipe.
A pretty big deal, all of this. And it doesn't look like this time it's just unfounded allegations.