Each of the 17 young men is seeking $20 million in damages.
Perlitz, 41, once hailed as a savior at the school, pleaded guilty to federal charges of sexual abuse and was sentenced to nearly 20 years in prison in December 2010.
Some of the boys, who have grown to adulthood, appeared in court for Perlitz's sentencing more than a year ago. Now, they want to be compensated.
Among those they are suing are Fairfield University, a Jesuit college in Fairfield, Connecticut, Paul Carrier, the school's former chaplain, The Society of Jesus of New England and The Haiti Fund Inc., a Connecticut-based nonprofit fund-raising arm of the Cap Haitien school.
The institutions are contesting their role in Perlitz's work in Haiti.
"The crimes to which Mr. Perlitz has admitted at Project Pierre Toussaint in Haiti are deeply disturbing," said Alice Poltorick, director of communications for The Society of Jesus New England. "That said, (Project Pierre Toussaint) was not a mission of the Society of Jesus of New England."
Fairfield University's lawyer said the school had no supervisory role at Project Pierre Toussaint.
"We feel that the case should be dismissed," said Stan Twardy.
The Haiti Fund did not respond to CNN's attempt for a comment.
The complaints filed Thursday painted a different picture.
The 17 men charged that the people and institutions they sued "aided and abetted" Perlitz in his acts and then helped conceal them.
Perlitz first arrived in Cap-Haitien in 1997. According to the federal indictment, Perlitz became inspired to build a school there.
He received a grant from the Roman Catholic Order of Malta to start a center to help street children, which grew into the Project Pierre Toussaint.
Perlitz took homeless boys off the street and gave them education, meals and a place to sleep.
"When I met Mr. Douglas, he appeared to us like Jesus Christ himself come to rescue us," said Francilien Jean-Charles, who was only 12 when he was plucked by Perlitz and brought to the school. He spoke with CNN at the time of Perlitz's sentencing.
Abuse lawyer Mitchell Garabedian, who filed the complaints Thursday, said Perlitz took advantage of poor boys.
"He would tell the children, 'if you do not let me sexually molest you, I will not give you food shelter or clothing,'" he said.
According to the federal indictment, Perlitz provided money and told one of the boys he would not be kicked out of the school even if he failed his classes.
He allegedly offered another boy and his family money and other benefits, and in another case gave a television, shoes, clothes and meals to another boy, in exchange for sexual favors and their silence.
Those who did not cooperate with Perlitz were denied the benefits, the indictment said. Perlitz frequently flew back to Fairfield, Connecticut, to raise money.
According to court documents, from 2002 to 2008, donors gave more than $2 million, Fairfield University awarded him an honorary degree in 2002, and Fairfield students volunteered at the school.
In 2002, Fairfield University honored Perlitz's efforts in Haiti by making him its commencement speaker.
Perlitz was arrested in 2009 after accusations of molestation surfaced.