Scott Roeder, 51, was charged with the first-degree murder of Dr George Tiller, who was shot dead on Sunday at a church in Wichita.
Mr Roeder is also charged with aggravated assault against two people who tried to intervene in the attack.
Mr Roeder is being held in a Wichita jail and appeared in Sedgwick County District Court, also in Wichita, via video link.
The suspect has requested a lawyer and has been assigned to the public defender's office, the Kansas City Star newspaper reported.
A preliminary hearing has been tentatively set for 16 June, the report added.
Mr Roeder was arrested in a suburb of Kansas City about 170 miles (274km) from the scene, some three hours after the shooting at the Reformation Lutheran Church.
Dr Tiller's clinic - Women's Health Care Services - had often been the site of demonstrations, and he had been shot and wounded by an assailant 16 years ago.
Following the fatal shooting, US Attorney General Eric Holder promised protection to "appropriate people and facilities".
Anti-abortion groups in the US have denounced Dr Tiller's killing.
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