Stanley Dishon, 55, of Bullitt County was indicted by a grand jury last week, and was arraigned in a Shepherdsville courtroom Monday, WDRB-TV, Louisville, reported.
A trial date for the case was scheduled for late April.
Dishon is accused of "sexual deviate intercourse" in 1996 and 1997 with a male relative under 12.
Last October, Dishon pleaded not guilty to the 1999 kidnapping and murder of his niece, Jessica Dishon, 17. Two inmates who served prison time with him claimed in interviews Dishon told them he murdered the girl to keep her from revealing a sexual relationship, the (Louisville) Courier-Journal reported.
Dishon was in a state reformatory after being charged in 2002 with sexually abusing two girls, 8 and 10.
He had nearly served his 10-year sentence when he was indicted last August for the 1982 sexual assault of a girl under 12. His trial for that indictment will begin Tuesday, the Courier-Journal said.