A High Court jury deciding whether an Auckland man is guilty of murdering his two-year-old stepson has retired for the night.

The jury at the High Court in Auckland is considering whether Joel Loffley, 29, murdered JJ Ruhe Lawrence, who died at his home in Orakei, east Auckland, on November 14 last year.

They went out to consider their verdicts about 2pm on Tuesday after Justice Patrick Keane summed up the trial, which is now into its third week.

They retired for the night at 5pm and are due to resume deliberations on Wednesday.

Justice Keane told jurors when summing up the case on Tuesday that emotions were understandable with the death of a two-year-old but they can't be ruled by them.

He also told them that though Loffley admitted violence on JJ's mother Josephine Lawrence and on previous partners and on having kicked some previous children in his care, they needed to consider what happened on November 14 as their primary task.

The Crown alleges that Loffley struck JJ with such force it was as if he'd been hit with a hammer, a blow which split his liver and pancreas in half.

Loffley's lawyer Roger Chambers said the Crown had not provided clear and compelling evidence that Loffley had killed JJ.