If Wednesday's decision "is allowed to stand it will effectively repeal the Fourth Amendment for confidential electronic records," union head Donald Fehr said in a statement on Thursday.
The court's 2-1 ruling could help authorities pinpoint the source of steroids in professional baseball. It also could bolster the perjury case against Giants slugger Barry Bonds, who is under investigation for telling a grand jury he never knowingly used performance-enhancing drugs.
Michael Rains, Bonds' attorney, disagreed. "It doesn't help their case against him," he said.
Fehr said he was consulting with union attorneys to "determine what our next step should be in our fight to protect the constitutional rights, including the basic right to privacy, of our members."
Options include asking the San Francisco-based 9th U.S. Circuit Court of Appeals to rehear the case with the same three judges, petitioning the court to hear the case with 15 judges or appealing to the U.S. Supreme Court. Any appeal, even if unsuccessful, could delay the government from getting the records for months or more.
The samples were collected at the league's direction as part of a survey to gauge the prevalence of steroid use. Players and owners agreed in their labor contract that the results would be confidential.
The players' union sued to keep the government from accessing the records, saying the seizures violated the players' constitutional rights.
Wednesday's 120-page decision overturned a lower court that sided with the players. U.S. District Judge Susan Illston of San Francisco had quashed the subpoenas, ruling they constituted harassment and were unreasonable.
U.S. Attorney Kevin Ryan of San Francisco praised the appellate court's finding that the government's "use of grand jury subpoenas were reasonable."
The government's investigation of the Bay Area Laboratory Co-Operative, a Burlingame supplements lab at the center of the steroid scandal, already has resulted in guilty pleas from BALCO president Victor Conte, Bonds' personal trainer Greg Anderson, BALCO vice president James Valente, chemist Patrick Arnold and track coach Remi Korchemny.
Indictments are pending against cyclist Tammy Thomas and track coach Trevor Graham.
The case is United States v. Comprehensive Drug Testing Inc., 05-10067.