Wesley Matthew King was accused of breaking into Lonsdale Street Roasters in late December 2014 and stealing $3900 cash, an EFTPOS machine, cash drawer, iPod, and keys to a Jeep from an office safe.

The cafe's manager discovered the crime when he arrived at the business on January 1 to find it ransacked with diarrhoea-like faeces smeared across papers on the floor next to a pair of stained underpants, the court documents said. The till and EFTPOS machine were missing.

DNA evidence taken from the pants' waistband indicated Mr King had worn them before, but the forensic scientist admitted another set of DNA found on the pants made it possible someone else could have worn the unwashed pants more recently.

Police were unable to find the identity of the other person linked to the pants.

Mr King chose not to give evidence during an ACT Supreme Court trial.

In a judgment published on Wednesday, Chief Justice Helen Murrell acknowledged DNA evidence suggested King had worn the pants, but found it wasn't enough to find him guilty of three counts of burglary and one count of theft.

"There is … 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 said.

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

The forensic scientist chose not to take a sample of the faeces for testing because bacteria was likely to degrade DNA with which it had come into contact.