The case against Clemens involved one count of obstruction of Congress, three counts of making false statements and two counts of perjury. He was not charged with illicit use of performance-enhancing drugs, but his denial of such use was part of the case against him.
A jury found him not guilty on all six counts.
Federal prosecutor Courtney Saleski, in closing arguments, told jurors Clemens "wanted to protect his brand, he wanted to protect his livelihood," in denying the use of steroids during a 2008 investigation by the U.S. House of Representatives into the problem.
The Clemens defense team disputed whether the government had made its case, telling the jury all the evidence came through a former personal trainer, Brian McNamee, who had incentive to lie.
"You saw Brian McNamee, the only witness in the history of the world who says he gave or saw an injection of that man," said defense attorney Michael Attanasio. "One person in the entire world." During closing arguments, the defense cited the lack of corroborating witnesses.
It took about eight weeks for the prosecution and defense to question 46 witnesses, and the most direct conflict came among expert witnesses as to how to interpret a collection of discarded medical items that allegedly linked Clemens to steroid use. The pitcher did not take the stand in his defense.
Soiled medical wrappings, cotton balls, drug vials and hypodermic needles that McNamee kept were interpreted differently by each side. Witnesses for the government said genetic material linked with Clemens suggested it was impossible for McNamee to fabricate the evidence.
But defense witnesses on the same topic said storage in a beer can for years allowed commingling and contamination of materials, making reliable conclusions impossible, and the evidence nearly worthless.
This was the second trial for Clemens. About a year ago, a mistrial was declared before the case reached the jury. The government's lawyers played video evidence the judge had already banned. Prosecutors said it was an editing mistake, but the Clemens defense team suggested prosecutors were unprepared and had gotten off to a bad start.
CNN's Paul Courson and Joe Johns contributed to this report.