Spanish colonial sites in southern Peru and Bolivia contain remains of native camelids and introduced bovids with examples of degenerative paleopathologies that are interpreted as reflecting changes in herd management, animal use and animal health following the Spanish conquest. The archaeological contexts include three Spanish colonial wineries from Moquegua in southern Peru and the nearby colonial village of Torata Alta where indigenous people were forced to resettle under Spanish control. Also from Peru is faunal material from the 14th to 16th century rural agropastoral village of Pillistay located near Camana. Animal remains with bone abnormalities are also present in residential, commercial and industrial sites associated with Spanish silver mining near Potosí, Bolivia at Tarapaya and Cruz Pampa. Eighteen pathological specimens are described including examples of degenerative changes to phalanges, vertebrae, tarsals, limb elements and ribs. Paleopathologies present include exostoses, osteophytes, porosity, grooving and eburnation. Examples of phalangeal exostoses on bovid phalanges indicate the use of these introduced animals as draught cattle. Exostoses on camelid first phalanges suggests their use as cargo animals as do thoracic vertebrae with severe cases of degenerative pathology. Introduced caprines contain few pathologies indicating their primary use as food animals. The bone abnormalities from colonial sites are more severe than those reported for prehispanic faunal assemblages. These data provide insights into the health and work behaviour of indigenous Andean camelids and introduced Eurasian animals following the Spanish conquest. Copyright © 2009 John Wiley & Sons, Ltd.