On Monday, US District Judge Sam Sparks dismissed Armstrong's 80-page lawsuit as a "lengthy and bitter polemic," but gave his lawyers up to 20 days to file an amended complaint.
The lawsuit refiled by Armstrong's lawyers at the US District Court in his hometown of Austin, Texas, was much shorter at 25 pages.
Armstrong faces a looming deadline on Saturday to either challenge the charges that he took performance-enhancing drugs, or accept sanctions that could strip him of his seven Tour de France titles and ban him from the sport for life if he is found guilty.
The USADA is a quasi-governmental agency created by Congress in 2000 and charges would be considered by its own arbitration process. Any penalties would be binding within the sport, but federal courts have the power to overrule the agency.
Lawyers for Armstrong contend that the USADA gathered evidence by threatening to ruin the careers of fellow cyclists who have agreed to testify against him. Lawyers for Armstrong also argue that the USADA's rules violate his right to a fair trial and that the agency lacks proper jurisdiction to charge him.
In a statement issued on Monday, the USADA said Armstrong's lawsuit is "without merit" and that USADA rules "provide full constitutional due process designed to protect the rights of clean athletes and the integrity of the sport."
Accusations of doping have dogged Armstrong since he ascended to the top of the cycling world after overcoming cancer. In February, the US Justice Department dropped an investigation centered on whether Armstrong and his teammates cheated the sponsor of their bike racing team, the US Postal Service, with a secret doping program.
But on Tuesday, three former Armstrong associates were handed lifetime bans for their involvement in an alleged doping conspiracy, the USADA said.
Team doctor Luis Garcia del Moral, consulting doctor Michele Ferrari and trainer Jose "Pepe" Marti were all banned from the sport for life after USADA found they had violated a series of anti-doping regulations.
- Sports & Recreation