Former church youth group leader Samuel Patrick Dockary is on trial in the Hamilton District Court on a raft of rape and sexual assault charges.

A former church youth group leader allegedly raped a girl and, when he thought she was pregnant, punched her in the stomach.

Samuel Patrick Dockary, 23, is facing 26 charges including rape, indecent assault, and unlawful sexual connection.

He pleaded not guilty at the beginning of his trial at the Hamilton District Court on Tuesday.

MARK TAYLOR/STUFF Samuel Patrick Dockary, 23, faces 26 charges including rape, indecent assault, and unlawful sexual connection.

The offences are alleged to have taken place in Auckland and Waikato between September 1, 2011 and March 1, 2013, and involve two complainants, both of whom were aged under 16 at the time.

Some of the charges Dockary faces are alternative charges to some of the more serious ones - which include two counts of rape.

Other incidents including the alleged molestation of the two complainants and instances where he had them perform oral sex on him.

Dockary is being represented by lawyer Sheila Cameron, who told the jury of five men and seven women that issues of consent would be at the heart of their decision-making process.

"It's not about applying morality, certainly not Christian morality," she said. "It's about applying common sense."

It was up to the Crown to disprove consent or prove indecency, Cameron said.

The Crown case in the seven-day trial is being handled by Rebecca Guthrie.

The court heard from one of the two alleged victims who, shielded from her alleged abuser by a screen, spoke of how he struck up a friendship with her, before obtaining her cellphone number and making romantic advances towards her through text messages.

"He said he wanted a relationship with me ... I was quite flattered [although] I thought it was strange and I was uncomfortable."

He also befriended the victim's family and began attending events such as family dinners.

It was at one such occasion where he groped the girl's breast while they were watching television.

Some time after he walked the girl home to her parents' house and he again began intimately touching her and tried to kiss her, in spite of her objections.

"He came in close to kiss me ... I said we are not supposed to do this.

"I did not know how to kiss anyone. I bit him on the lip."

Further alleged incidents followed, with Dockary becoming increasingly persistent. On one occasion he allegedly forced her to give him oral sex, telling her it was her "job" to fellate him.

She said she had wanted to vomit and was scared of how aggressive he had become.

Dockary was initially living in a dormitory on the church campus, but eventually moved into a flat a short distance away. He used to pick up the girl and take her back to his flat, where their sexual activity continued - including one incident where he allegedly raped her.

"He at one stage believed I was pregnant. He was quite paranoid."

Dockary then allegedly punched her in the stomach.

"He said 'If there is a baby in there, I have just killed it," she said.

She had tried to end the relationship, however she was scared that Dockary would hurt himself if that happened.

The trial, under Judge Kim Saunders, continues.