A Cecil County grand jury handed up indictments against Dr. Steven Brigham of Voorhees, N.J. and Dr. Nicola Riley, of Salt Lake City, Utah.
Both doctors are being held in their home states awaiting extradition hearings.
The indictments cap a 16-month investigation. The investigation began in August 2010 after a botched procedure at Brigham's clinic.
An 18-year-old woman who was 21 weeks pregnant had her uterus ruptured and her bowel injured, and rather than call 911, Brigham and Riley drove her to a nearby hospital, where both were uncooperative and Brigham refused to give his name, authorities said.
When authorities searched the clinic after the botched abortion, they found a freezer with 35 late-term fetuses inside, including one believed to have been aborted at 36 weeks.
At least one case involved a woman who was critically injured during the procedure.
Brigham, 55, is charged with five counts of first-degree murder, five counts of second-degree murder and one count of conspiracy. Riley, 46, faces one count each of first- and second-degree murder and one conspiracy count.
Maryland is one of 38 states with a law that allows murder charges against someone accused of killing a viable fetus. The 2005 law has so far only been used for cases in which defendants were accused of assaulting or killing pregnant women.
The Associated Press contributed to this report.