This study analyzes oral pathological conditions—caries, antemortem tooth loss, and occlusal macrowear—among adults (N = 70) interred at Machu Picchu, Peru. Previous isotopic diet reconstructions at Machu Picchu suggest substantial early‐life variation that may have narrowed somewhat by the last decade of life. This study seeks to further elucidate the intersection of diet, sex, and health at Machu Picchu by analyzing oral pathological conditions with existing carbon and nitrogen isotopic data. Observed caries prevalence is corrected to control for age and tooth loss, and is described for both anterior and posterior teeth; wear data are scored and reported for individual tooth types. Results indicate caries prevalence consistent with carbohydrate‐rich diets and no significant difference between males and females. However, no significant isotopic parameters are associated with caries prevalence in young adult males, while caries prevalence is significantly associated only with enamel carbonate δ13C in older adult males. Dietary protein sources, but not C4 resources, are associated with caries prevalence in young adult females, and to a lesser degree in older adult females. Significant associations between occlusal wear and caries exist among young adult males and young adult females, but involving different tooth types. These findings suggest differential protein consumption at Machu Picchu between males and females, and separate masticatory and physiological processes shaping caries prevalence between the sexes at the site. This study therefore underscores the role that gender roles may have played in diet variation among this population and the need to account for sex in analyzing oral pathology. Copyright © 2013 John Wiley & Sons, Ltd.