A judge has dismissed an application to stay charges in a historic sexual assault case in Windsor.

Justice Renee Pomerance delivered the ruling against John Thomas Wuschenny on Wednesday. AM800 News reports the ruling allowed closing submissions to be heard.

Wuschenny’s lawyer, Andrew Telford-Keogh, argued the five charges should be stayed because of "unacceptable negligence" on the part of police.

Wuschenny, 57, has pleaded not guilty to sexual assault, forcible confinement, break and enter, disguising himself and threatening death, after a woman told police she was assaulted in her home on Marentette Avenue in 1990.

Wuschenny wasn't charged until 2016, after his DNA was found on a shirt.

But testimony during the trial revealed an evidence control sheet, which logged the evidence from the case, is now missing.

Telford-Keogh argued they don't know who seized the shirt and where it was stored between 1990 and 2016, when DNA on the shirt was tested again and led to Wuschenny's arrest.

But Crown attorney Walter Costa argued it doesn't change the fact Wuschenny's DNA was found on the shirt and neither he nor the victim had a previous relationship before the alleged assault.

Justice Pomerance will hand down her decision November 14 at 9 a.m.