It’s the second time in two months the court has cited debate over the diagnosis of shaken baby syndrome.

BOSTON —A man convicted of severely injuring his girlfriend’s 2-year-old daughter by violently shaking her must get a new trial, the highest court in Massachusetts ruled Thursday, the second time in two months the court has cited heated debate in the medical community over the diagnosis of shaken baby syndrome.

In its latest ruling, the court found that there was a “substantial risk of a miscarriage of justice” in the trial of Derick Epps because his attorney did not call an expert to try to challenge testimony from a prosecution expert who said the girl’s injuries were consistent with shaken baby syndrome. Epps told police the girl fell down the stairs and also fell off a kitchen stool and hit her head.

“We conclude that, in the unusual circumstances of this case, the absence of expert testimony that the child’s injuries might have been caused by her accidental falls deprived the defendant of an available, substantial ground of defense and thereby created a substantial risk of a miscarriage of justice,” Chief Justice Ralph Gants wrote for the court in the unanimous 6-0 opinion.

The court cited its ruling last month in the case of Oswelt Millien, who was convicted in 2010 of violently shaking his infant daughter, who suffered head and neck injuries. In that case, the court also overturned the conviction, noting the ongoing debate over whether strong shaking alone can generate enough force to cause the symptoms of traumatic brain injury and whether the symptoms can sometimes be caused by a short accidental fall.

Epps was convicted of assault and battery for injuring the girl in 2004. She remains paralyzed on her right side, cannot walk and is blind in one eye, the court said in its ruling.

The Supreme Judicial Court said at the time of the 2007 trial, “there was substantial scientific and medical literature that recognized the possibility that accidental short falls can cause serious head injuries in young children of the type generally associated with shaken baby syndrome.”

In the Millien case, the Supreme Judicial Court noted that judges in Utah and Michigan have issued similar rulings in other cases in recent years.