In many high-income countries, indigenous populations bear a higher burden of obesity and diabetes than non-indigenous populations. Less is known about these patterns in lower- and middle-income countries. We assessed the hypothesis that obesity and diabetes were less prevalent among indigenous than non-indigenous adults in Mexico, home to the largest indigenous population in Latin America. We investigated socioeconomic explanations for differences. In a related line of inquiry, we examine whether adults in communities with higher versus lower percentages of indigenous residents were buffered against these conditions. We assessed whether differences were partially explained by lower development in higher-indigenous communities. Obesity was based on measured height and weight, and diabetes on a diagnosis from a healthcare professional. The analysis for obesity included 19 577 adults aged 20 and older from the Mexican Family Life Survey (2002), a nationally representative survey of Mexican households and communities; for diabetes, we restricted analysis to adults with health insurance. We used multilevel logistic regression to estimate the odds of obesity and diabetes by indigenous status and community percent indigenous. Results suggest that indigenous adults had significantly lower odds of obesity and diabetes than nonindigenous adults. This advantage was not explained by the lower socioeconomic status of indigenous individuals. A higher percentage of indigenous individuals in communities provided protection against obesity, although not for diabetes. Differences for obesity were not accounted for by community. Findings suggest that an opportunity may exist to prevent disparities in obesity and diabetes from developing by indigenous characteristics in Mexico. Identifying the sources of protective effects of individual and community indigenous characteristics relative to these health conditions should be a priority, given global implications for prevention.