Dr. Kermit Gosnell was also found guilty of involuntary manslaughter in the overdose death of a patient.
Prosecutors say the 72-year-old Gosnell delivered babies alive and had their spines severed with scissors to kill them. They say the baby whose death he was cleared in let out a soft whimper before Gosnell cut its neck.
The defense had argued there were no live births at the clinic.
The grisly details of the case came out more than two years ago when authorities described finding bags and bottles of fetuses at the foul-smelling clinic and unsterile instruments that were reused.
Prosecutors seek the death penalty.