We show the potential of paleomagnetism applied to sediments filling cave passages for chronology purposes, since the formation of caves cannot be directly dated. The Atapuerca karst system (N Spain) offers a suitable case scenario because it contains a multilevel karst system developed during the progressive incision of the Arlanzón River. This karst formed during the Quaternary in response to the incision of this tributary of the Duero River in the Cenozoic continental deposits. We present new magnetic polarity results from both clastic and chemical deposits from cavities of the Atapuerca karst. These deposits provide minimum ages for the multilevel karst development, and they have implications for the incision history and water-table evolution during the Pleistocene. We find that the karstification of the studied levels developed during the Matuyama chron, before the middle Pleistocene, as suggested by the magnetostratigraphic and also cosmogenic burial ages of sediments infilling the karstic passages.