The case against Clemens involved one count of obstruction of Congress, three counts of making false statements and two counts of perjury. He was found not guilty on all counts.
He was not charged with illicit use of performance-enhancing drugs, but his denial of such use was part of the case against him.
Arguments in the trial in Washington concluded last week.
Federal prosecutor Courtney Saleski, in closing arguments Tuesday, told the jury 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 has made its case, telling the jury all the evidence came through a former personal trainer, Brian McNamee, who the defense team said had incentive to lie.