Objectives This study examines biological indicators of dental disease and nonspecific stress in human remains of three high altitude Himalayan archaeological sites to test whether shared ecological constraints led to similar bioarchaeological profiles in these markers. Methods Samples (n = 170) derive from three sites in Nepal dating to two periods (400–50 BCE and c. 400–650 CE). Dental diseases (caries, antemortem tooth loss, and abscesses) were assessed by both the number of individuals and the number of elements observed, while childhood stress markers included observation of growth disruptions (enamel hypoplasia and adult femur length/stature) and cranial porosities. Statistical analysis included chi‐square and Fisher's exact tests for categorical data and ANOVA and t‐tests for metric data. Results There are significant differences between the sites and sexes in frequencies of dental diseases in the adult samples. There are low frequencies of childhood stress markers overall and the femur length data show no significant differences across sites, but significant sexual dimorphism within each site. Females have reduced stature compared to contemporary Tibetan samples residing at a similar elevation. Conclusions Variations in dental disease frequencies between the sites may be due to local variations in microenvironment, cultural, and/or temporal differences in resource availability, food consumption and preparation, as well as the age structure of the samples. The low frequencies of markers for nonspecific stress may be indicative of the ability of these ancient Himalayan groups to successfully meet the challenges posed by the extreme conditions of high altitude living through biocultural adaptations.