In 1979, according to 2007 court testimony, Gambino boss John Gotti retaliated against Agnello for assaulting his daughter, Victoria Gotti. Several Gambino associates ambushed Agnello, beat him with a baseball bat, and then shot him in the buttocks. In 1984, Agnello married Victoria. The couple had three sons, Carmine Agnello, John Agnello, and Frank Agnello, and a stillborn daughter, Justine. The family lived in a mansion in Westbury, New York that was the location in 2004 for the reality television series, Growing up Gotti.
On February 5, 1994, Agnello was charged with criminal mischief for damaging a police scooter. The officer was ticketing cars parked outside of Agnello's scrapyard. Agnello came out to argue with the officer, then started his Ford Bronco and rammed the police vehicle, pushing it 15 feet (4.6 m) down the street. In June 1994, Agnello and several Gambino members brawled with police outside the same location, again over parking tickets, and Agnello was again arrested. On June 6, 1997, Agnello was arrested on assault charges for beating a former employee with a telephone. The victim later decided to drop the complaint.
On January 20, 2000, Agnello was charged with racketeering and arson. Undercover New York Police Department (NYPD) officers had set up a phony scrap metal business in Willets Point, Queens. Agnello then used firebombings and other illegal tactics to coerce them to sell their scrap to him at a below-market price. According to testimony, Agnello promised a cooperating witness $2000 to "buy glass bottles (and) fill them up (with gasoline) and throw them all around the truck" of a competitor. Defense documents claimed that Agnello was on medication for bipolar disorder, which led him to bad judgement. On August 16, 2001, Agnello accepted a plea bargain in return for a reduced sentence.
On October 26, 2001, Agnello was sentenced to nine years in federal prison and ordered to forfeit $10 million in assets to the court. He was released from federal custody on January 16, 2008.
In 2003, Victoria Gotti divorced Agnello on grounds of constructive abandonment (no sexual relations for more than a year) because he was in jail. Before the divorce, it was alleged that Agnello had been dating another woman.
On February 19, 2008, Agnello quietly married Danielle Vangar, the daughter of activist Mourad "Moose" Topalian. Vangar met Agnello in prison when she was visiting her father.  Agnello and Vangar have a son, who was born in 2009, Agnello and his second family live in Ohio. He owns a business in Ohio that tows junk cars.
In July of 2015, Agnello was arrested in Cleveland, Ohio on charges of theft, money laundering, and conspiracy, as well as drugging race horses.
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