Holder told Republicans on the committee the Justice Department does not inform the White House of ongoing investigations.
He also said he didn't participate in the decision to subpoena phone records from the AP.
Holder told the House Judiciary Committee, "I was recused in that matter. ... I am not familiar with the reasons why the subpoena was constructed in the way it was. ... [However] I have faith in the people who were responsible in this case."
The subpoena for phone records of about 20 AP employees came in the investigation of media leaks of U.S. Justice Department information.
Holder was questioned closely on the subpoena by House Judiciary Chairman Bob Goodlatte, R-Va., and other Republicans.
Holder said he withdrew from the process because "I am a fact witness in that I am a possessor of the information that was leaked." He confirmed that the subpoena process was overseen by Deputy Attorney General James Cole.
The department hasn't revealed details of the leak investigation.
U.S. Rep. Jerrold Nadler, D-N.Y., said there was irony in that last year Republicans on the committee had "demanded an investigation of press leaks" and prosecution of media violators but now were lambasting the Justice Department for the leaks investigation.
Goodlatte said in a statement the department should be involved in protecting free speech, not chilling it.
"Any abridgment of the First Amendment is very concerning, especially reports that the IRS targeted conservative groups for unwarranted scrutiny during an election year," Goodlatte said.
Holder said Tuesday his department would open an investigation into whether Internal Revenue Service officials broke laws by singling out conservative groups.