Paleoecological and taphonomic analysis of the mammalian microfauna from three Bolivian altiplano sites is presented: Khonkho Wankane [Late Formative period; number of identified specimens (NISP) = 1019], Mollo Kontu (Middle Horizon period; NISP = 610) and Pukara de Khonkho (Late Intermediate period; NISP = 165). The following species, all of which are present in this region today, were identified: Akodon boliviensis (Bolivian grass mouse), Andinomys edax (Andean mouse), Auliscomys sublimis (Andean leaf‐eared mouse), Cavia porcellus (guinea pig/cuy), Chinchilla chinchilla (chinchilla), Ctenomys leucodon (white‐toothed tuco‐tuco), Eligmodontia puerulus (Andean gerbil mouse), Galea musteloides (common yellow‐toothed cavy), Lagidium viscacia (vizcacha), Neotomys ebriosus (Andean swamp rat),and Oligoryzomys destructor (destructive pygmy rice rat). Some direct human involvement with the deposition of some of the larger species (Cavia porcellus, Chinchilla chinchilla, Ctenomys leucodon and Lagidium viscacia) was noted, although C. porcellus was identified only from a single element from Mollo Kontu. Most deposition was likely due to natural in‐burrow deaths and other natural attrition of these species. No significant shift in environment during the occupation of these sites was detected. Copyright © 2012 John Wiley & Sons, Ltd.