There was an extremely strong chance DNA found inside the underpants of a five-year-old girl came from the man accused of abusing her, a court has heard.

But the ACT Supreme Court has been told tests for saliva turned up nothing, despite the girls allegation her step-grandfather licked her vagina.

And the court has heard tests werent carried out on other items of clothing and bedding because they were likely to be covered in his DNA and have no probative value.

The underpants were also placed in the same bag as another item of clothing, prompting the defence to suggest the DNA might have transferred from one to the other.

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The 61-year-old man, who cannot be named, is on trial in front of Justice Richard Refshauge accused of two counts of having sexual intercourse with a child.

He has pleaded not guilty, and also denies two alternative charges of committing acts of indecency on the girl.

It is alleged he licked the girls vagina twice when he was babysitting her in April 2009.

The allegations came to light after the girls mother picked her up, when the girl asked her mother if she could tell her the secret she shared with poppy.

The accused man entered the witness box this afternoon and denied any wrongdoing, describing his shock when police confronted him with the allegations.

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Court hears DNA findings in child sex case