There was overwhelming evidence of a double murder in the Sally Clark case, the General Medical Council has heard.
Sally Clark was freed in January 2003
Home Office pathologist Dr Alison Armour was giving her view during the case of Dr Alan Williams.
Home Office forensic pathologist Dr Williams, 58, is alleged to have botched post-mortem examinations on Mrs Clark's children in 1996 and 1998.
Dr Williams, of Plumley, near Knutsford in Cheshire, denies serious professional misconduct.
He is also accused of not disclosing evidence that could have helped clear Mrs Clark, who was wrongly convicted of the murders of 12-week-old Christopher and his eight-week-old brother, Harry, in 1999.
Mrs Clark, a solicitor from Wilmslow, was cleared by the Court of Appeal in 2003.
At first, Dr Williams said Christopher had died of a lung infection, but changed his mind after Harry's death, and claimed he was smothered.
He told Mrs Clark's murder trial that Harry appeared to have been shaken to death but he did not keep proper records of tests he carried out, throwing doubt on the quality of his work, the GMC had heard.
Dr Williams examined both of Mrs Clark's sons
Microbiology results from Harry's post-mortem examination suggested he may have died from an infection with a bacterium called staphylococcus aureus, but Dr Williams did not disclose this at Mrs Clark's committal, to the police or the Crown Prosecution Service.
Dr Armour told the GMC on Wednesday the presence of bacteria during a post-mortem test did not mean there was an infection.
She said in 1998 she would have referred to the microbiology results, but insisted there was no evidence of infection.
But she added: "There are still a number of facts that are there to support a diagnosis of shaken baby syndrome - swelling to the spinal cord, extradural haemorrhaging around the spinal cords, bleeding into the optic nerve.
"My view is by the time Dr Williams came to do the autopsy of Harry Clark the evidence that he was dealing with a double homicide was in my view overwhelming."
She claimed there was "sufficient evidence" for shaken baby syndrome in Harry's case.
She added that in her opinion Christopher's death was "unascertained".