Neil Miller was convicted of aggravated rape while armed and breaking and entering with intent to commit a felony on December 19, 1990, in Boston, Massachusetts. He was sentenced to twenty-six to forty-five years in prison.

A man brandishing a screwdriver forced his way into the victim's apartment where he robbed and raped her vaginally and forced her to perform oral sex. The victim picked Miller's photo out of a mug book after he had been convicted of a non-sexual crime. Miller's conviction rested almost entirely on the eyewitness testimony of the victim. His defense at trial was mistaken identification. Miller claimed that he had never seen the victim before or been in her apartment.

A scientist from the Boston Police Crime Laboratory testified at trial that semen stains were found on the victim's bedding with B and H blood group substances. A vaginal swab with semen contained H blood group substances. Both the victim and Neil Miller are type O secretors, so the testing did not eliminate him. PGM testing was done on the bed sheet and no PGM was found. Neil Miller was PGM-1 and the victim was PGM 2-1. No PGM testing was done on the swabs.

The Innocence Project opened Miller's case in 1998. The vaginal swabs and smears from the initial evidence was located and sent to Forensic Science Associates. FSA's test results definitively excluded Neil Miller from being the source of spermatozoa found. Neil Miller, after over nine unjust years in prison, was exonerated and released in 2000.