Dr. Michele Ferrari, a consultant; Dr. Luis Garcia del Moral, team doctor; and Jose "Pepe" Martí were part of a large-scale doping conspiracy, according to the USADA. The agency says Armstrong, who won six Tour de France championships while with U.S. Postal, was also involved in doping.
Each was given a Monday deadline to accept sanctions or contest the charges. Armstrong was granted a five-day extension.
Among the charges against the two doctors and Marti was the accusation that they trafficked performance-enhancing drugs and masking agents.
Lance Armstrong faces new doping claims "Permanently banning these individuals from sport is a powerful statement that protects the current and next generation of athletes from their influence, and preserves the integrity of future competition," USADA CEO Travis Tygart said in a written statement.
Former USPS team manager Johan Bruyneel and Dr. Pedro Celaya also have been charged by the USADA.
The agency's release did not specify whether they also were granted extensions for their cases or had opted for an arbitration hearing.
On Monday, a federal judge threw out Armstrong's lawsuit against the U.S. Anti-Doping Agency, blasting the seven-time Tour de France champion in a sharply worded ruling.
Armstrong filed the case Monday morning in his hometown of Austin, Texas, in a bid to halt a doping case against him.
In his brief order, U.S. District Judge Sam Sparks wrote that the case was full of legally irrelevant claims "included solely to increase media coverage of this case" and stir up hostility toward the USADA.
"This court is not inclined to indulge Armstrong's desire for publicity, self-aggrandizement, or vilification of defendants, by sifting through 80 mostly unnecessary pages in search of the few kernels of factual material relevant to his claims," Sparks wrote.
He urged the cyclist to re-file his lawsuit without "any improper argument, rhetoric, or irrelevant material."
"Contrary to Armstrong's apparent belief, pleadings filed in the United States District Courts are not press releases, internet blogs or pieces of investigative journalism," the judge added in a footnote. "All parties, and their lawyers, are expected to comply with the rules of this court, and face potential sanctions if they do not."
The USADA has accused Armstrong of using performance-enhancing drugs.
The 40-year-old cyclist, who is now competing in triathlons, had asked the court to file an injunction against the USADA by Saturday, the agency's deadline for Armstrong to either contest the charges or accept sanctions.
Armstrong maintains he has never tested positive for performance-enhancing drugs and said the USADA and its CEO, Travis Tygart, are out to get a "big fish" to justify the agency's existence.
"Defendants have charged Mr. Armstrong with unspecified doping violations and seek to try him through USADA's self-created, self-regulated and self-operated process that it has rigged to ensure that it cannot lose," the lawsuit says. "USADA's kangaroo court proceeding would violate due process even if USADA had jurisdiction to pursue its charges against Mr. Armstrong."
In June, the agency announced that it was opening proceedings against Armstrong and five former teammates. In a statement issued in response to the lawsuit, Tygart said the agency "was built by athletes on the principles of fairness and integrity."
"Like previous lawsuits aimed at concealing the truth, this lawsuit is without merit and 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," he said.