The witness, who cannot be named for legal reasons, had a statement about his time at St Columba’s in Largs, North Ayrshire, read to the Scottish Child Abuse Inquiry yesterday.
The man, now in his 50s, claims to have suffered a serious sexual assault at the hands of a monk before enrolling at the school.
He told how his family had a strong connection with the Marist order, which ran the establishment, and they had gone on a trip to Middlesbrough with a religious brother.
The witness, who was then aged seven, said: “It was then that he betrayed my trust, (he) took me up to his room.
“He had been drinking heavily, he made me carry out acts of a sexual nature on him.
“I was naked from the waist down, he then raped me.”
It was heard he attended the school in the 1960s and 1970s and feared being sexually assaulted again during his first two years there, but this did not happen.
He also told how he believed his mother had been having sex with the same monk.
The witness said: “I have suspicions my mother had a relationship with (him) and he was my biological father.
“When I was 12, I thought he was visiting my mother for sex.Why else would he be there?”
Meanwhile, another victim told how sexual abuse at the hands of a former teacher became “normalised”, happening several times a week.
The witness was first admitted to the establishment in 1978 and stayed until 1982.
The inquiry heard the witness had his bed sprayed with water by the man during the night and was then made to go into the former teacher’s bedroom.
He said: “I remember having to take my clothes off and I think on that occasion he made me stay in there and had to sleep on the edge of the bed in front of him.”
That was the first time he suffered sexual assault, he said.
But the witness claimed the abuse went on throughout his time at the boarding school, being made to perform acts on another boy as well.
He added: “It was constant, I’m not saying every day, but a number of times a week.
“It just seemed to be something that was part of life at the school.”
The witness also spoke of being told about the death of schoolboy Aldo Moroni, after hearing wailing from a pupil in the building.
He said: “There was a boy screaming upstairs, like he was in pain. Some of us started to go upstairs, a lad started shouting at the boys to get back down the stairs.
“Within a number of days, we were told he was dead.”
The inquiry, before judge Lady Smith in Edinburgh, continues on Tuesday.