Johnson County prosecutor Phill Kline charged the clinic with 23 felony counts and 84 misdemeanor counts, according to court records. Besides 29 misdemeanor counts of providing unlawful late-term abortions, the clinic is charged with multiple counts of making a false writing, failure to maintain records and failure to determine viability.
Case documents have been sealed, according to a court order. The first hearing is set for Nov. 16.
Kline's office did not immediately comment on the charges.
Peter Brownlie, president and chief executive officer of Planned Parenthood of Kansas and Mid-Missouri, said Wednesday that the group hasn't had any contact with the district attorney's office but has heard rumors for months that Kline, an abortion opponent, was planning to file criminal charges.
"I've heard nothing at all about specific charges that have been filed," Brownlie said in a telephone interview. "We always provide high-quality care in full accord with state and federal law."
As for allegations that Planned Parenthood performed illegal late-term abortions, Brownlie said its clinic doesn't perform any past the 22nd week of pregnancy.
Attorney General Paul Morrison previously reviewed all of the allegations upon which Kline's criminal charges are based and found no wrongdoing, Morrison spokeswoman Ashley Anstaett said.
"The attorney general did a thorough review of Planned Parenthood and found no wrongdoing," Anstaett said. "We are skeptical that these charges have any merit, and we continue to wonder how much politics influenced Mr. Kline's decision to file these charges."
Kline's charges came less than four months after Morrison closed his investigation and told Planned Parenthood's attorneys that he found no wrongdoing by the clinic or its personnel.
Morrison reviewed records Kline had obtained as attorney general. Elected to the statewide office in 2002, Kline began an investigation into Planned Parenthood and a clinic operated in Wichita by Dr. George Tiller a few months after taking office; a legal dispute over the clinics' records lasted more than two years.
Morrison, an abortion rights Democrat, defeated Kline, a Republican seeking his second term, in the November election.
Morrison had previously served as Johnson County district attorney, winning elections in the county as a Republican before switching parties to challenge Kline. Local GOP activists then picked Kline to fill the county vacancy.
Kline, Morrison and Planned Parenthood are embroiled in another lawsuit pending before the Kansas Supreme Court. Planned Parenthood sued Kline, and Morrison later successfully intervened on the state's behalf.
Documents in that case remain sealed as well, and neither Kline nor Planned Parenthood have discussed it.
But Morrison warned Planned Parenthood's attorneys in June that Kline appeared to still have access to copies of patient records he had obtained as attorney general.
Morrison said those records were forwarded from the attorney general's office to the district attorney's office a few day before Kline left the attorney general's office.