A Rochester man pleaded not guilty Thursday morning to several counts of sexual abuse against three children.

John Knowlton, 40, is accused of predatory sexual assault against a child, rape, incest, criminal sexual act and endangering the welfare of a child.

Prosecutors say the abuse happened over several years in the Northwest part of the city.

"It literally started for two of them as long as they can remember," said prosecutor Kyle Rossi. "The proof will show it began when they were five and continued up until his arrest September 18th."

Rossi said at one point during those years, there were allegations of abuse. He says there was an investigation but nothing was ever prosecuted. This time, he said one of the children disclosed at school and the investigation led to an arrest.

"Just reading the allegations, the period of time that's involved, the nature of the acts; if these prove to be true, it's almost unimaginable that someone would do this, that children are forced to live in this way."

Knowlton's cousin Donna Colaianni said she was shocked when learning of the charges. She said she was glad he was arrested.

"Thank God. Good. I hope he gets 25 to life. No man should ever do that to other children. That's disgusting."

Judge Vincent Dinolfo issued orders of protection for the children and told Knowlton he is to have no contact with them or anyone else connected to them. Rossi said in court Knowlton may have been trying to contact people to tell the children to "change their stories."

Rossi said the children are somewhere safe and getting help.

"In Monroe County, we have an excellent system to try to combat this and try to make kids whole again. Every resource we have available, we have made available to these children."

Knowlton's attorney Liz Riley told YNN they're just starting to get all the information of the allegations and have to continue their own investigation into what happened. She said these are often complicated cases and it can be dangerous to rush to any judgement.

Knowlton pleaded not guilty to all the charges and is in jail without bail. He's due back in court in December.