Gosnell was also convicted of involuntary manslaughter in the death of a female patient who died after receiving a dose of sedatives and pain killers in a 2009 abortion. He was acquitted in the death of a fourth baby.
The 72-year-old doctor had little reaction when the verdicts were announced.
The jury reached a decision after deliberating for 10 days in the case that became a flashpoint in the nation's debate over abortion. For two months, the jury heard grisly testimony about the filthy clinic in an impoverished section of West Philadelphia described in a grand jury report as a "house of horrors."
Former clinic employees testified that Gosnell routinely performed illegal late-term abortions past Pennsylvania's 24-week limit, that he delivered babies who were still moving, whimpering or breathing, and that he and his assistants "snipped" the newborns' spines, as he referred to it.
Prosecutors said none of the staff were licensed nurses or doctors.
Bags and bottles of stored fetuses were found at the clinic, according to authorities, as well as jars of severed feet, bloodstained furniture, dirty medical instruments and cats roaming the premises.
Gosnell's defense maintains that the doctor served his community and never killed a live, born baby, claiming that any movements were posthumous twitching or spasms.
Jurors will return Tuesday to hear evidence on whether Gosnell should get the death penalty.
Pennsylvania authorities had failed to conduct routine inspections of all of its abortion clinics for 15 years by the time Gosnell's facility was raided and closed down. In the scandal's aftermath, two top state health department officials were fired, and Pennsylvania imposed tougher rules for clinics.
Four former clinic employees have pleaded guilty to murder and four more to other charges. They include Gosnell's wife, Pearl, a cosmetologist who helped perform abortions.
Gosnell still faces federal drug charges. Authorities said that he ranked third in the state for OxyContin prescriptions and that he left blank prescription pads at his office and let staff members make them out to cash-paying patients.
The Associated Press contributed to this report.