Kyle Campbell, 26, and Kayleigh Siswick, 27, appeared at Leeds Crown Court today over the death of Siswick's three-year-old son Riley in February, 2016.
Riley was found unresponsive at his home address in Smiths Avenue in Marsh on February 6 and was pronounced dead at the scene.
A court previously heard that he had suffered blunt force trauma.
Campbell and Siswick spoke only to confirm their names, dates of birth and nationalities and to enter pleas during a 15-minute hearing.
The pair, both of Heys View in Huddersfield, denied a total of five charges.
Campbell pleaded not guilty to murder and an alternative charge of causing or allowing the death of a child.
Siswick pleaded not guilty to causing or allowing the death of a child.
Campbell also pleaded not guilty to two counts of assault occasioning actual bodily harm in relation to another child.
A pre-trial review was listed for April 12 next year.
A trial was listed for May 20 next year is expected to last between six to eight weeks.
Campbell was returned to custody. Siswick was released on conditional bail until the next hearing.