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.
The hearing continues.