Houck left the office on Wednesday, but tendered his resignation some time earlier. A press spokesperson could not confirm if Houck resigned before closing arguments on September 21.
The landmark antitrust case, in which the Justice Department and 19 states allege Microsoft unfairly used its Windows monopoly against browser rival Netscape, is before U.S. District Judge Thomas Penfield Jackson.
Jackson could render a preliminary judgment in a matter of weeks, although antitrust experts speculate he will wait longer if he thinks there is any chance of settlement. The judge has strongly encouraged the parties to settle.
The New York Attorney General's office downplayed the impact of Houck's departure on the case.
"We don't see any impact on the trial," said Juanita Scarlott, spokeswoman for the New York Attorney General's office. "Harry First, who is a prominent antitrust lawyer, was overseeing the trial, the case, and all the cases from the antitrust bureau. We have complete confidence he will continue to represent the attorney general's office in all matters."
Houck, who played a more behind-the-scenes roll in the case, did not garner the same attention as the Justice Department's attorney, David Boies.
Boies drew attention during cross-examination of Microsoft witnesses. He caught Microsoft senior vice president Jim Allchin in an embarrassing gaffe with video evidence that riveted the courtroom and drew the ire of Jackson.
Boies questioned all but one of the 26 witnesses, IBM executive John Soyring, who was questioned by Houck.
Houck did play an important role in closing arguments, where he and Boies laid out a compelling argument for Microsoft's monopoly power.
Houck described Microsoft as an "emperor without clothes. No matter how loudly Microsoft proclaims it is not a monopoly, we know and Microsoft knows it is a monopoly." Microsoft's attorney John Warden disagreed with the assessment, arguing Microsoft does not fit the economic definition of a monopoly.