The USADA sent a 15-page letter to Armstrong alleging blood samples from Armstrong were "fully consistent with blood manipulation."
The USADA letter accuses Armstrong of using and promoting the use of the blood booster EPO, blood transfusions, testosterone, human growth hormone and anti-inflammatory steroids. Blood samples reportedly include some from Armstrong's Tour de France races
Armstrong is a seven-time Tour de France champion. He would face a lifetime ban from cycling if found guilty of using performance-enhancing drugs.
Due to Wednesday's USADA charges, Armstrong has been banned from competing in triathlons, which he took up after retiring last year.
USADA's letter to Armstrong informing him of the charges also said the agency was bringing doping charges against Johan Bruyneel, manager of Armstrong's winning teams; team doctors Pedro Celaya and Luis Garicia del Moral; team trainer Pepe Martin, and consulting doctor Michele Ferrari.
In February, federal prosecutors closed a two-year criminal investigation of doping charges against Armstrong. Armstrong was not indicted.
Armstrong released a statement Wednesday in response to the USADA charges:
"These are the very same charges and the same witnesses that the Justice Department chose not to pursue after a two-year investigation. ...
"Although USADA alleges a wide-ranging conspiracy extended over more than 16 years, I am the only athlete it has chosen to charge. ...
"I have never doped, and, unlike many of my accusers, I have competed as an endurance athlete for 25 years with no spike in performance, passed more than 500 drug tests and never failed one."
The USADA oversees anti-doping in Olympic sports in the United States. It cannot bring criminal charges.
The Associated Press contributed to this report.