Federal prosecutors conducted the 2004 raid, seeking the players’ urine samples from 2003, in an effort to verify whether Bonds and nine others testified truthfully before the Balco grand jury.  The samples and test results the prosecutors sought were part of the anonymous testing that Major League Baseball had conducted in 2003 in its first step toward combating the use of performance-enhancing drugs in baseball. Under the testing guidelines, every player on a major league team’s 40-man roster was tested at least once; about 240 players were subjected to a second, random test. Not even the players were supposed to know the test results.  Under an agreement between baseball and its players union, stricter testing, with penalties, would begin in 2004 only if more than 5 percent of the 2003 tests turned up positive. In the end, 5 percent to 7 percent of the 1,438 tests in 2003 were positive. Baseball then adopted testing with penalties.  Left unanswered was why the players union did not have all of the 2003 urine samples and test results destroyed once the anonymous testing had been completed and the percentage of positive tests had been compiled. Samples from players who did not test positive were supposed to be destroyed after 30 days. Why Bonds’s negative sample from 2003 was not destroyed is not known, but it now looms large in his case.  Before the 2004 raid, the prosecutors tried a less confrontational approach, issuing a subpoena for all the samples and the results from the 2003 testing. After Comprehensive Drug Testing and Quest Diagnostics, the two companies that conducted the anonymous tests, refused to relinquish them, the prosecutors narrowed the subpoena to the samples and the results for the 10 players who had testified before the Balco grand jury.  The players union told the federal government that it would seek to quash the subpoena. The government then secured search warrants to obtain the samples and test results for the 10 players; the federal agent Jeff Novitzky carried out the raid the next day.  But even with agents at two sites, finding the samples they wanted proved difficult. Because the tests were supposed to remain anonymous, the urine samples were not labeled with players’ names. The urine samples were kept at a Las Vegas location for Quest Diagnostics, and a list with players’ names and corresponding code numbers was kept at Comprehensive Drug Testing’s facility in Long Beach, Calif.  When Novitzky and other agents went to Comprehensive Drug Testing, the employees would not help them, but during their search of the lab, the agents discovered a master list of all the players who had tested positive in 2003. A raid designed to find the results and samples of the 10 players connected to Balco had now produced far more than that.  The federal agents who raided Quest Diagnostics in Las Vegas, armed with the code numbers obtained at Comprehensive Drug Testing, seized the matching urine samples for the 10 players. A month later, agents went back and took the urine samples for all the players who tested positive in 2003.  The fact that Bonds’s 2003 urine sample did not result in a positive when baseball tested it raises questions about whether other players might have avoided detection that year. On Tuesday, Rob Manfred, an executive vice president for Major League Baseball, said that after the 2003 seasons, baseball switched from Quest Diagnostics to the World Anti-Doping Agency’s laboratory in Montreal.  “We switched to the Wada laboratory because they are the gold standard of testing for performance-enhancing drugs,” Manfred said.  Although the 2003 sample from Bonds is now being contested by defense lawyers, it is not specifically cited in their motion. But language in the motion alludes to the 2003 urine sample by quoting from a letter written by prosecutors that is not part of the public record.  In that letter, the prosecutors addressed the chain of custody of urine samples for Bonds and said they could be verified by the “agents who transported the samples.” According to one of the people briefed on the investigation, those words refer to the 2004 raid.  A version of this article appears in print on , on Page B10 of the New York edition with the headline: Bonds’s Urine Retested, And Result Is a Positive. Order Reprints| Today's Paper|Subscribe
After an anonymous urine sample from 2003 was tested for performance-enhancing drugs, Barry Bonds lawyers and federal prosecutors battle over whether it can be used as evidence at his trial.