Dr. Kermit Gosnell, 72, still faces the death penalty if convicted of first-degree murder in four remaining infant deaths. The judge also upheld murder charges in a patient's overdose death.
Prosecutors have argued that the babies were viable and Gosnell and his staff cut them in the back of the neck to kill them.
Common Pleas Judge Jeffrey Minehart did not explain his reasoning for the split decision on the defense motion to acquit Gosnell after five weeks of prosecution testimony. Such requests are routine but rarely granted.
The defense questioned testimony from staffers who said they had seen babies move, cry or breathe. McMahon argued that each testified to seeing only a single movement or breath.
"There is not one piece - not one - of objective, scientific evidence that anyone was born alive," McMahon said. "These are not the movements of a live child."
The trial was set to resume Tuesday afternoon with defense witnesses for Gosnell's co-defendant, Eileen O'Neill. She is charged with three counts of theft for practicing medicine without a license. Minehart dismissed six additional counts of that charge.
Gosnell must defend a third-degree murder charge for the 2009 overdose death of 41-year-old Karnamaya Mongar, a recent refugee to the U.S. who died after an abortion.
McMahon argued that third-degree requires malice, or "conscious disregard" for her particular life.
"She wasn't treated any differently than any of the other thousands of other people who went through there," McMahon argued.
Assistant District Attorney Ed Cameron, in defending the murder charge against Mongar, said it stemmed from the totality of the circumstances. They included the repeated medication dosages given by medical assistants; Gosnell's absence during most of her visit; and the hour it took to open a locked side door and take her by stretcher to an ambulance.
Prosecutors might concede that point, while arguing 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 Gosnell was offsite, and were then left in waiting rooms, sometimes unattended, for hours before Gosnell arrived for the late-night surgeries.