James P. Eaton is charged with first-degree intentional homicide and hiding a corpse. Online court records say he pleaded not guilty Wednesday.
Messages left with his two public defenders were not immediately returned.
The 36-year-old from Palatine, Ill., was arrested in Chicago this month. He's accused of killing Amber Creek, a 14-year-old also from Palatine. Her battered body was found in a Racine County marsh.
Police were unable to develop a suspect for years. They say a federal DNA database connected Eaton to the crime in February, and that investigators confirmed by tailing him and recovering DNA from a cigarette he discarded.