A man accused of defecating during a burglary at a Canberra coffee shop has been found not guilty, despite his soiled underpants being found at the scene of the crime.

Wesley Matthew King was charged with four counts of burglary-related offences after a Braddon cafe was broken into in late 2014.

When police investigated the break-in they found a pair of soiled underpants in the shop's office, along with papers smeared with faeces.

Nearly $4,000 cash, an iPod and car keys were stolen from the office safe, while an EFTPOS machine and till drawer were missing from the cafe.

DNA tests on the underpants concluded they belonged to Mr King; however, the ACT Supreme Court found that was not enough to prove he was responsible for the break-in.

Tests on the underpants found the DNA of another person, but police were not able to identify them.

In her judgment, Chief Justice Helen Murrell said she could not discount the possibility that someone else had been wearing Mr King's dirty underpants.

"I am not satisfied that guilt is the only available rational inference," she wrote.

"There is, for example, a reasonable [albeit small] possibility that the burglar was someone else who was wearing unwashed underpants that had previously been worn by the accused."

She found Mr King not guilty of all charges.