Armstrong asked the court to issue an injunction by Saturday, the deadline he faces to formally challenge the case in USADA's arbitration process or accept sanctions. He could receive a lifetime ban from cycling and be stripped of his Tour de France victories if found guilty.
Armstrong insists he is innocent.
"The process (USADA) seek to force upon Lance Armstrong is not a fair process and truth is not its goal," his lawsuit says, calling the USADA process a "kangaroo court."
Tygart said Armstrong's lawsuit is "aimed at concealing the truth" and predicted a judge will rule in the agency's favor.
"USADA was built by athletes on the principles of fairness and integrity," he said in a statement. "We are confident the courts will continue to uphold the established rules which provide full constitutional due process and are designed to protect the rights of clean athletes and the integrity of sport."
USADA, created in 2000 and recognized by Congress as the official anti-doping agency for Olympic sports in the United States, formally charged Armstrong in June with taking performance-enhancing drugs and participating in a vast doping conspiracy on his Tour de France winning teams, some of which were sponsored by the U.S. Postal Service.
The charges came after a two-year federal criminal investigation into doping allegations against Armstrong ended in February with no charges filed against him. The anti-doping agency says up to 10 former teammates and associates are willing to testify against him and that it has blood samples from 2009-2010 that are "fully consistent" with doping.
Armstrong, who retired in 2011, says he has passed more than 500 drug tests in his career and was never flagged for a positive test.
Armstrong's lawsuit amplifies public complaints he made about USADA and Tygart in recent weeks and makes several arguments. It says:
• The agency's rules and arbitration are designed to find athletes guilty. Athletes are not allowed to subpoena documents or compel witnesses to testify in a hearing. USADA has so far withheld the names of most of the witnesses against Armstrong, saying it is protecting them from potential intimidation.
The International Cycling Union, cycling's governing body which licensed Armstrong to ride professionally, should have jurisdiction over the allegations. Armstrong says allegations of doping by him and his team that were first raised by admitted drug-user Floyd Landis in 2010 should be addressed by UCI.
• USADA may have violated federal law if it coerced witness testimony against him with deals to reduce punishments for riders facing doping charges. Media reports last week said former Armstrong teammates George Hincapie, Levi Leipheimer, David Zabriskie and Christian Vande Velde, who are all riding in this year's Tour de France, may be witnesses against him.
• Tygart and officials with the World Anti-Doping Agency have recklessly pursued Armstrong for several years in a personal quest to catch him despite Armstrong's hundreds of negative drug tests. Tygart was named a co-defendant in the lawsuit.
Also charged by USADA are former Armstrong team manager Johan Bruyneel and several team doctors and associates. None of them are included in Armstrong's lawsuit.
Armstrong's lawsuit says he faces irreparable harm if the case is allowed to go forward to arbitration because USADA rules prevent him from being able to mount a legitimate defense.
"It is a testament to USADA's brazenness and callous disregard for its own mission that it seeks to strip Mr. Armstrong of his life's work," the lawsuit says.
There was no immediate indication when a judge would rule. The case was filed in U.S. District Court in Austin.