Gavin John Gosnell, 28, denies killing the 15-year-old on or about August 22, 2011.
He pleaded not guilty in the High Court at Christchurch this morning and will be represented by defence counsel Craig Ruane.
Hayden Miles, a schoolboy, was reported missing after going to a friend's house in Cashel St, Linwood on August 22.
After a four-month missing persons inquiry, his remains were found at nearby Ruru Lawn cemetery.
Crown prosecutor Barnaby Hawes in his opening address told the jury this morning that Gosnell had "severely assaulted" Hayden at a city flat on August 22.
The next day he "began a process of dismembering Hayden Miles's body" before cutting him into 12 parts, Mr Hawes said.
He then dumped the body parts at two city cemeteries nearby, he said.
Gosnell sat in court, his hair tied back in a ponytail, and wore a striped shirt buttoned up to his neck.
Justice Lester Chisholm told the jury that the Crown must prove that Gosnell is guilty beyond reasonable doubt.
He added that while he will explain the law to the jury, they must then apply it to the facts.
"You are the judges of fact," he said.
Justice Chisholm warned the jury that some of the things they will hear and see will "not be pleasant".
But he stressed the importance of not being swayed by prejudice or sympathy, and urged them to keep an open mind.
The trial continues.
