Pathological conditions in human skeletal remains provide a wealth of information about archaeological populations, but many are limited in their interpretive significance by their nonspecific etiologies. This study analyzes three common pathological conditions known to manifest in infancy and childhood in the skeletal population from Machu Picchu, Peru (N = 74) with published carbon, nitrogen, oxygen, strontium, and lead isotopic data (Turner et al.: J Archaeol Sci 36 (2009) 317–332; Turner et al.: Chungara: Revista de Antropología Chilena 42 (2010) 515–524) to distinguish early-life diet from residential origins as significantly associated with pathologies among the site's inhabitants. Analyses of variance indicate highly significant variation between enamel δ18O values, which serve as a rough proxy of local environment, and both cribra orbitalia (CO) and porotic hyperostosis (PH), generally understood to be markers of anemia. Results tentatively suggest that individuals manifesting these lesions may have lived closer to the arid coasts; however, no significant variation was found in parameters of diet (enamel δ13Ccarbonate, dentin δ13Ccollagen, dentin δ15N) by either CO or PH, suggesting that the primary factors causing anemia may have been more significantly related to residential origin rather than diet. Linear enamel hypoplasia (LEH) frequency significantly varied by both dietary and residential parameters, supporting models of LEH formation from a synergy of dietary and environmental factors. These results support previous research on the etiology of PH in the Andes; they also represent a useful approach to refining site-specific interpretations of pathological conditions in archaeological populations, and exploring etiological variation between populations. Am J Phys Anthropol, 2012. © 2012 Wiley Periodicals, Inc.