The parents of Queensland teenager Daniel Morcombe have come face to face with their son's alleged killer.

The long-awaited trial of the man accused of murdering Daniel on the Sunshine Coast began today in Brisbane.

A 15-person Supreme Court jury, including three reserves, was empanelled before the lunch break while Brett Peter Cowan looked on from the prisoner's dock.

The hearing resumed this afternoon with Justice Roslyn Atkinson explaining to the jurors what they must consider before deciding whether or not Cowan is guilty.

Justice Atkinson has also taken them through the elements of murder and the lesser charge of manslaughter that they must consider before deciding upon their verdicts.

Six jurors were excused from the trial this morning amid concerns about their impartiality.

Daniel Morcombe was 13 when he vanished while waiting for a bus under the Kiel Mountain Road overpass at Woombye on December 7, 2003.

He had been planning to go Christmas shopping.

It sparked the biggest police investigation in Queensland history, with the boy's remains found near the Glass House Mountains eight years later.

Cowan, 44, is charged with murder, indecent treatment of a child and interfering with a corpse.

Cowan, also known as Shaddo N-Unyah Hunter, entered not guilty pleas to all charges when he was arraigned under both names this morning.

The former tow truck driver walked past the Morcombe family in the public gallery before entering the prisoner's dock, dressed in a grey sports coat and navy pants.

Moments later, Daniel's mother Denise Morcombe left the court room clearly upset, with her husband Bruce.

Denise and Bruce Morcombe outside Brisbane's Supreme Court today. ( AAP: Dan Peled )

Prosecutor Glen Cash read out the witness list of 158 people who could be called during the trial.

The Morcombes are expected to be among the first witnesses called to give evidence.

Arriving at the court this morning, Mr Morcombe said he was looking forward to the outcome.

The trial is expected to last up to six weeks.

Prosecutor Michael Byrne QC will open the case against Cowan tomorrow morning, followed by an address from Cowan's lawyer, Angus Edwards.

The Morcombes are expected to attend the trial with family and friends for as many days as possible.

A private room has been set aside for them if they need to use it.

Another room has been set aside for the media to watch proceedings.

Police Commissioner Ian Stewart says officers are well prepared for the start of the high-profile case.

"This trial has been a long time coming, I know," he said.

"The whole Queensland community - in fact the Australian community - is watching with interest.

"Obviously we have to go through the court process, but I'm hopeful we'll be able to put the very best case to the court."