Barry 'Budgie' McCarney, 33, from Woodview Crescent, Trillick, who denies the charges of murder and sexually and physically abusing the youngster, was asked if he would go into the witness box on Monday.
He was warned by Judge Justice Stephens it could go against him if he did not give evidence.
McCarney is on trial at Dungannon Crown Court along with the child's 27-year-old mum, Rachael Martin, from Main Street in Kesh, who is accused of wilfully neglecting and allowing the death of the 15-month-old from severe head injuries in the early hours of 11 December 2009. She also denies the charges.
Following a week of unconnected legal argument, Mr Justice Stephens was told on Monday morning by defence QC Elis McDermott that McCarney would not be giving evidence, nor would any other evidence be called on his behalf.
Mr Justice Stephens then asked Ms McDermott if McCarney had been advised of what might flow from his decision in not taking the stand, and his refusal to answer any questions put to him.
In the circumstances, the judge said it would be open to the jury of nine men and three women to "draw such inferences from McCarney's refusal that appear proper for them to do so".
Later Rachael Martin gave evidence on her own behalf.
She began by describing her developing relationship with McCarney, who started dating her after he'd sought her father's permission.
When asked by her defence QC John McCrudden, if it had "ever crossed your mind that your little girl" was being abused, what would she have done, Martin replied: "It never crossed my mind at all, if it ever entered my head he would not have been in my house".
Questioned about the night before Baby Millie was rushed to hospital, Martin refuted McCarney's claims to police that the youngster was 'limp' and appeared to be 'loaded with the flu'. Martin maintained her daughter was "100 percent".
Rejecting McCarney's claims as being "nothing could be further from the truth", and repeated: "Millie was perfect".
However, she admitted that the following morning she was "surprised" as it appeared Baby Millie was "coming down with the cold".
She added that when she took her to her mother's house, both she and her mum had "cried" over Baby Millie's condition.
"I never seen Millie ill before and it broke my heart for her to look like that," claimed Martin.
However the toddler appeared to pick up, "sometimes smiling", while at other times she was "sleepy, wanting cuddles all the time".
Later when she put Baby Mille to bed, Martin said she gave her a kiss and the youngster smiled at her when she told her she loved her and would see her in the morning.
But she never saw her in her cot again, because while she was out buying McCarney a Kit-Kat, he was rushing Baby Millie to hospital.
While Martin claimed that what happened "in the hospital is all a blur", she said that she "couldn't believe it" when she was told by medical staff her daughter had been sexually abused.
"I really couldn't believe it - I couldn't digest it," said Martin who added that her family decided to keep the fact to themselves, because she didn't want "McCarney to flee".
Martin said that the family knew both the police and Social Services "were on their way" and that "he was going to be arrested".
Her defence lawyer Mr McCrudden will continue questioning Martin on Tuesday after which she will be cross-examined by McCarney's QC Elis McDermott and prosecuting QC Carian Murphy.