Understanding the cause of patchy bone distributions in archaeological sites requires that one distinguish bone decomposition in place from “empty” areas where bones were never present. Marked horizontal variations in bone abundance are found in the thick Mousterian layer (E) of Hayonim Cave, a large Paleolithic site in northern Israel. Infra-red analyses of minerals in the sediments identify zones of advanced diagenesis and decomposition alongside zones whose chemistry clearly favoured the preservation of bones and wood ash. These differences adhere closely to the distribution of recognizable bones in the deposits, indicating that spatial variation in bone abundance is essentially a product of differential preservation conditions. However, the few bones present in the bone-poor units are in surprisingly good condition. The higher degree of abrasion damage and more random orientations of these bones indicate that small amounts of recent material were introduced into older layers by small burrowing animals and perhaps localized trampling. The ratio of post-Mousterian to Mousterian artifacts in layer E, and the numeric contrasts in bone abundance among stratigraphic units, indicate that time-averaging from mechanical intrusion was quantitatively unimportant (2–5%) throughout this>2·4m thick layer. Our findings support Karkanas et al. (2000) suggestion that bone and ash mineral diagenesis in caves follow step-wise rather than gradual transformations in geological time. Good preservation environments can be distinguished from poorer ones on the basis of mineral assemblages in sediments, and deposits that once contained bone and wood ash can be identified long after the visible traces of these materials have disappeared.