Conquest of indigenous peoples in North America is understood primarily through ethnohistorical documents, archaeological evidence, and osteological analyses. However, in the Central Andes, the colonial enterprise and its effects are understood only from postcontact historical and ethnohistorical sources. Few archaeological and bioarchaeological studies have investigated Spanish Conquest and colonialism in the Andean region [for exceptions see Klaus and Tam: Am J Phys Anthropol 138 (2009) 356–368; Wernke, in press; and Quilter, in press]. Here we describe bioarchaeological evidence of violence from the cemeteries of Huaquerones and 57AS03 within the archaeological zone of Puruchuco-Huaquerones, Peru (circa A.D. 1470–1540). A total of 258 individuals greater than 15 years of age were analyzed for evidence of traumatic injuries. Individuals were examined macroscopically and evidence of traumatic injuries was analyzed according to the skeletal element involved, the location of the injury on the skeletal element, and any additional complications of the injury. This study examines and compares the evidence of perimortem injuries on skeletonized individuals from the two cemeteries and focuses specifically on the interpretation of weapon-related perimortem injuries. Evidence of perimortem trauma is present in both cemeteries (18.6%, 48/258); however, the frequency of injuries in 57AS03 is greater than that in Huaquerones (25.0% vs. 13.0%). Several injuries from 57AS03 are consistent with documented cases of injuries from firearms and 16th Century European weapons. We believe that the nature and high frequency of perimortem trauma at 57AS03 provide evidence of the violence that occurred with Spanish Conquest of the Inca Empire. Am J Phys Anthropol 142:636–649, 2010. © 2010 Wiley-Liss, Inc.