A doctor said she suspected child abuse on examining the body of Poppi Worthington, who was 'probably' sexually assaulted by her father before her death.
Home Office pathologist Alison Armour said further post-mortem examination showed the 13-month-old had reddened inner thighs and bruising and small tears to her rectum, Kendal Coroner's Court heard.
The otherwise healthy toddler collapsed at home in Barrow, Cumbria, and was pronounced dead in hospital an hour later.
Her father Paul Worthington, 49, was ruled to have probably sexually assaulted her, according to a judge during family court proceedings.
Detectives at Cumbria Police, who dismissed Dr Armour's initial view as "rash", botched their investigation which meant vital evidence was lost.
Mr Worthington, who is now in hiding, has never been charged with any offence and denies any wrongdoing. The cause of Poppi's death remains "unascertained".
Last week he refused to answer questions 252 times at the inquest, using his legal right not to potentially incriminate himself.
On Monday, Dr Armour stood in front of post-mortem photos of the youngster's body, shown on a large TV monitor in court, to explain her findings.
She said she was given a verbal briefing by police before the post-mortem examination began and was aware that Poppi had leg injuries before her death from earlier X-rays.
Alison Hewitt, counsel to the inquest, asked the witness: "Do you recall whether you expressed any view as to whether this is a case of child abuse?"
Dr Armour said there was no record of any accident to explain the leg injuries, which were only picked up after Poppi's death.
She added: "I was very concerned about the healing fractures to the right tibia and fibula and my remarks were made to that effect - 'This is strongly suspicious of child abuse'."
Her post-mortem examination also found bruising to the back of Poppi's throat and external and internal injuries to her anus and rectum area.
Earlier, the inquest, which started last week, heard that, in the early hours of December 12 2012. Poppi's mother was asleep downstairs when she heard a scream which was followed by Mr Worthington coming down to fetch a clean nappy.
Shortly afterwards Mr Worthington he rushed back downstairs holding his lifeless daughter and shouting to his ex-partner to call for an ambulance.
This second inquest into Poppi's death was ordered after the controversial first hearing - held by a different coroner - was shrouded in secrecy and lasted just seven minutes.
Later, in a fact-finding judgment as part of care proceedings involving Poppi's siblings, family court judge Mr Justice Peter Jackson, now Lord Justice Peter Jackson, said Poppi's "significant bleeding" within 15 minutes of the 999 call made from the family home could only be explained sensibly as the result of penetrative trauma.
Poppi's DNA was also found on Mr Worthington's penis, which he said was by transfer from him holding the child and then going to the lavatory at the hospital.
Following day-long questioning of the pathologist, Dr Armour maintained she was "sure" Poppi had been penetrated prior to her death.
She told the hearing: "It is my view that the findings are indicative of injury. Injury to the anal rectum junction. It is my opinion it was an erect penis or penis shaped object which is responsible for this."
But she said penetration in this manner, even for a baby, would not necessarily cause death.
She said there were no natural causes to account for Poppi's death and that left her with two possible modes of dying in this case, a reflex cardiac arrest or asphyxia, but she could not be sure and so she had to conclude the cause of death remains "unascertained".
Dr Armour said that blood in the girl's nose is a sign of acute upper airways obstruction, seen in cases of smothering or suffocation.
But she added: "In this case there are signs of asphyxia, I have to be sure in this matter, and I can't be.
"I do not know the exact reason or the mechanism as to the death of Poppi Worthington. I can't be sure to the standard of proof required of me."
The hearing was adjourned until tomorrow morning when the witness will be questioned by Paul Worthington's lawyers.
Copyright (c) Press Association Ltd. 2017, All Rights Reserved. Picture (c) PA Wire.