Two people and a police officer with the University of Colorado in Colorado Springs were killed in the rampage, law enforcement officials said.
The university police department identified the officer killed as 44-year-old Garrett Swasey, a six-year veteran of the force.
The university says Swasey had gone to the clinic to support Colorado Springs police after he learned of the shooting.
Nine other people, including five police officers, were shot and are in good condition, police said.
The gunman is in custody. His name was not immediately released.
Authorities said they haven't determined a motive or whether the shooter had any connection to Planned Parenthood.
"We don't have any information on this individual's mentality, or his ideas or ideology," police Lt. Catherine Buckley said, ABC-affiliated WCBV TV station reported.
For several hours, the firing of a long gun was the only indication police had that the shooter was in the building, Buckley said. Officers finally made voice contact by shouting to him and convinced him to surrender, she said.
Three officers were shot while responding just before noon to the initial report of shots fired. More than two hours later, the gunman shot another officer in an exchange with police inside the clinic, Buckley said.
The suspect surrendered about five hours after entering the building.
The location of the shooting is less than 6 miles from the street where a man shot and killed two of three people before dying in a gun battle with police on Halloween day.