The three students and the victim are members of the track team.
Thomas Brady 16,.Boubacar Diallo 16 and Pier Berksmans 17 are charged with forcible touching, hazing, assault and more.
The victim, a freshman at the school says on several occasions the teens performed sexual acts on him and at one point threatened to rape him.
This afternoon at the school many students would not talk about the incident.
The teen suspects pleaded not guilty to the charges and are due back in court on Friday.
A letter was sent home with students telling parents about the allegations.
In a statement the Department of Education said
“An allegation was brought to Bronx High School of Science last Wednesday and three students were arrested. The matter is under investigation.”