A Suffolk Superior Court judge on Monday ordered Matthew Nilo, accused in a series of alleged rapes and assaults dating back to 2007 and 2008, held on $5 million bail during an arraignment Monday.

Nilo pleaded not guilty to the charges this morning. He can be released if he posts $500,000 cash.

Nilo is charged with three counts of aggravated rape, two counts of kidnapping, one count of assault — attempted rape and one count of indecent assault and battery. The charges stem from alleged incidents in the Terminal Street area of Charlestown on Aug. 18, 2007; Nov. 22, 2007; Aug. 5, 2008; and Dec. 23, 2008, according to information provided by BPD Commissioner Michael Cox last week.

An attorney now practicing in New Jersey, Nilo, 35, was arrested last Tuesday at his home in Weehawken, N.J., and agreed to waive extradition during a court appearance there last week.

The charges against Nilo were filed after Boston Police, working with the FBI, turned to genetic analysis of evidence that remained after the initial investigation of the assaults.

Boston Police, agents and analysts in the FBI’s Boston and Newark, N.J., field offices; and the Hudson County, N.J., Sheriff’s Office were involved in his  arrest last week.

Nilo had not posted bail, as of yet. His is due in court next on June 12.

– Developing