Arriving at Enniskillen Courthouse from Maghaberry Prison, where he has been on remand since the toddler's death in December 2009, Barry McCarney shouted at waiting journalists: "I'm completely innocent of all these allegations being made against me."
Inside Court 2, he stood in the dock flanked by two prison officers.
On the other side of the room stood his co-accused, Millie's 26-year-old mother, Rachael Martin.
McCarney was not Millie's father but at the time of her death had been living with Martin in a house at Glebe Park in Enniskillen.
Neither of them objected to the holding of a Preliminary Enquiry, when a District Judge decides, on the basis of witness statements and other documents, whether there is sufficient evidence against a defendant to return them for trial at a Crown Court.
McCarney listened as the clerk of the court read the four charges against him.
He is accused of sexually penetrating 15-month-old Millie with a part of his body between December 8 and 11, 2009, when he then allegedly murdered her. He is also charged with unlawfully and maliciously causing her grievous bodily harm between December 10 and 11, and her death by an unlawful act on December 11.
Asked if he wished to say anything in response to the charges, McCarney replied: "Yes I do. I would like to say I'm totally innocent of all charges. I didn't lay a hand on Millie. I'm sickened and saddened by the death of Millie."
The clerk then read the two charges against Millie's mother, who is heavily pregnant.
Martin is accused of failing to protect her daughter from the unlawful act that caused her death on December 11, and wilfully neglecting her in a manner likely to cause her unnecessary suffering, between September 1, 2009, and December 12, 2009.
Asked if she wished to say anything in answer to the charges, she replied: "No."
McCarney and Martin declined to give evidence or call witnesses at this stage in the legal proceedings.
Defence barrister, Mr. Garvan Duffy, told the court McCarney "completely denies all allegations of wrong doing".
Martin's solicitor, Mr. Aubrey Murray, made a similar submission, saying she "absolutely denies the allegations".
Deputy District Judge Paul Conway ruled that McCarney and Martin had a case to answer.
He returned then for trial at Omagh Crown Court on March 22.