The woman became suspicious when she found the toilet seat left up.
A 31-year-old man has been arrested after his ex-girlfriend found him standing in the middle of her bedroom, US media reports.
Cary Cocuzzi, 31, has been charged with burglary and unlawful restraint after he grabbed the woman's face, which prompted her to push him aside and run outside calling for help.
Concerned neighbours then called the police, who found Cocuzzi hiding under a pile of clothes.
After being arrested, he told officers he was homeless and had been sneaking in and out of the house for about two weeks.
Speaking to media in Pittsburgh, Pennsylvania, the mother-of-two said she'd been noticing strange things around her house including finding a blanket on the floor and seeing the toilet seat left up.
She told Channel 11: "I feel like this is going to affect me for the rest of my life.
"I had an intuition about it but I ignored it, I brushed it aside. I didn't want to seem paranoid but I should have trusted my instincts, because I was right."
The woman already had a protection from abuse (PFA) order against Cocuzzi after he tried to sexually assault her in the past, police said.
She added: "Nobody in my home uses the bathroom that way and I didn't have any visitors so I just thought, gosh, is this guy in my house? This is so strange.
"I knew that blanket had not been there before, I knew it. But what could I do? I already had the PFA against him."
She said her two daughters were not at home on the night Cocuzzi was discovered.