A judge has thrown out three of eight murder charges in the high-profile trial of a Philadelphia abortion provider accused of killing babies allegedly born alive at his clinic.

Dr Kermit Gosnell, 72, still faces the death penalty if convicted on four remaining counts of first-degree murder involving babies allegedly killed with scissors after being born alive.

The judge also upheld murder charges in a patient's overdose death.

Judge Jeffrey Minehart did not explain why he dismissed the counts, but apparently felt he had not heard sufficient evidence from prosecutors that those three babies were viable, born alive and then killed.

Much of the evidence during the five-week prosecution case has come from the recollection of former staff members, though their testimony was bolstered by graphic photographs of some of the aborted babies.

Prosecutors argued that the babies were viable and that Dr Gosnell and his staff cut the back of their necks to kill them.

"Why would you cut a baby in the back of the neck unless you were killing it?" Assistant District Attorney Ed Cameron asked.

The defence questioned testimony from staffers who said they had seen babies move, cry or breathe.

Defence attorney Jack McMahon argued that each testified to seeing only a single movement or breath.

"These are not the movements of a live child," Mr McMahon said.

"There is not one piece, not one, of objective, scientific evidence that anyone was born alive."

Dr Gosnell is also charged with third-degree murder in the 2009 death of 41-year-old Karnamaya Mongar, a recent refugee to the US from Bhutan who died after an abortion at his Women's Medical Society.

Mr McMahon argued that third-degree requires malice, or "conscious disregard" for her life.

"She wasn't treated any differently than any of the other thousands of other people who went through there," Mr McMahon argued, in a preview of his likely closing arguments.

Prosecutors might concede that point themselves at closings, and argue that patients were routinely exposed to unsanitary, intentionally reckless conditions at the clinic.

Former staffers have testified that patients received heavy sedatives and painkillers from untrained workers while Mr Gosnell was offsite, and were then left in waiting rooms for hours, often unattended, before Dr Gosnell arrived for the late-night surgeries.