The judges will be replaced by outside jurists, the Pennsylvania court system announced.
The judges have no known connections to Sandusky or the university, but the judges bowed out "to avoid any appearance of conflict of interest due to real or perceived connections" to Sandusky, according to a press release from the Administrative Office of Pennsylvania Courts.
Sandusky has maintained he is innocent of the 40 criminal counts against him for the alleged sexual abuse of eight boys over a 15-year period.
He remains free on bail, but he could end up in jail if new charges are filed. His attorney said he feared if new charges are filed, a judge could set bail so high that Sandusky couldn't pay it.
The Associated Press contributed to this report.