A man told a Vatican court on Wednesday how a former papal altar boy sexually abused him over a period of six years while both were teens attending a pre-seminary.

The alleged victim, now 30, took the stand in the trial, which represents the first time the Vatican has criminally prosecuted alleged acts of clerical sex abuse or their cover-up on its territory.

The alleged victim, identified by the initials L.G., has accused Gabriele Martinelli of assaulting him while both were enrolled at the St Pius X pre-seminary. The institution located on Vatican grounds hosts boys interested in the priesthood.

Martinelli, who is now a priest, has denied the accusations and has testified that they are part of a smear campaign against him. 

L.G. was 13 at the time the alleged abuse began and Martinelli 14. 

L.G. described how his "shock" turned into eventual "resignation" after the first episodes of sexual abuse, which he said began in late 2006 or early 2007, just months after he entered the pre-seminary. 

"Martinelli crawled into my bed at night," he told the court. "It was a very strange thing for me. I was little and had never been exposed to the world of sexuality.

"At home, or in my town, I had never heard of sex. I felt confused, I didn't understand what was going on." 

Afterwards, Martinelli left "like nothing happened", L.G. said. 

L.G. said the acts of touching continued two or three times a week, while his two roommates slept, or pretended to sleep, before Martinelli began demanding oral or anal sex.

The witness described how during a mass at St Peter's, as the altar boys waited in a corridor, Martinelli approached him. 

"This time he turned to me with his robe open and he was nude underneath. He invited me to follow him into one of the two bathrooms. I was shocked, these things during mass too?" L.G. said. 

In 2009, L.G. said, he spoke about Martinelli to the pre-seminary's former rector, Father Enrico Radice. Radice is a co-defendant in the trial for allegedly hushing up the affair and shielding Martinelli from justice. 

But he did not go into specifics and did not bring up the abuse, L.G. said: "At 30 years old I also feel guilty for not being clearer."

After leaving the pre-seminary, L.G. tried to block Martinelli, who was calling and sending messages to him, he said.   

Defence lawyers for Martinelli, however, showed contacts made by L.G., such as wishing him a happy birthday on Facebook, a text message asking for help finding a room to rent in Rome, and a long message on Facebook Messenger accusing Martinelli of being jealous of L.G.'s friendship with another former altar boy. 

Under Pope Francis and his predecessor Benedict XVI, the Vatican has taken an increasingly harder line against clerical sex abuse and cover-ups, after repeated worldwide scandals.

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