The religious symbol violates the constitutional guarantee of separation of church and state, according to the federal suit filed by the American Civil Liberties Union Foundation of Southern California.
"Placing a cross, the universal symbol of Christianity, back on the seal communicates that Los Angeles County favors and endorses one religion above all others. This is unconstitutional," ACLU chapter executive director Hector Villagra said in a statement.
The seal is used on county buildings and vehicles. The original seal, adopted in 1957, had a cross over the Hollywood Bowl. It was removed when the seal was redesigned in 2004 after the ACLU threatened legal action.
County supervisors voted 3-2 last month to put a cross atop the seal's depiction of historic San Gabriel Mission.
Supervisors Michael D. Antonovich and Don Knabe argued that the mission didn't have a cross when the seal was redesigned in 2004 but it does now and the seal should reflect that for accuracy.
"Once again, the ACLU storm troopers are attempting to rewrite history," Antonovich said in a statement. "However, just as other California municipalities have missions on their seals, Los Angeles County will prevail."
The cross had been removed from the mission when it underwent earthquake retrofitting. The cross was stolen, retrieved and restored to the mission in 2009.
Knabe said he was disappointed by the "frivolous" lawsuit.
"Our motion to add the cross to the county seal was in the name of historical correctness, not political correctness," he said in a statement.
The ACLU statement contended, "Historical accuracy, however, does not trump the Constitution."