We sought to evaluate whether residence at high altitude is associated with the development of obesity among those at increased risk of becoming obese. Obesity, a leading global health priority, is often refractory to care. A potentially novel intervention is hypoxia, which has demonstrated positive long-term metabolic effects in rats. Whether or not high altitude residence confers benefit in humans, however, remains unknown. Using a quasi-experimental, retrospective study design, we observed all outpatient medical encounters for overweight active component enlisted service members in the U.S. Army or Air Force from January 2006 to December 2012 who were stationed in the United States. We compared high altitude (>1.96 kilometers above sea level) duty assignment with low altitude (<0.98 kilometers). The outcome of interest was obesity related ICD-9 codes (278.00-01, V85.3x-V85.54) by Cox regression. We found service members had a lower hazard ratio (HR) of incident obesity diagnosis if stationed at high altitude as compared to low altitude (HR 0.59, 95% confidence interval [CI] 0.54–0.65; p<0.001). Using geographic distribution of obesity prevalence among civilians throughout the U.S. as a covariate (as measured by the Centers for Disease Control and Prevention and the REGARDS study) also predicted obesity onset among service members. In conclusion, high altitude residence predicts lower rates of new obesity diagnoses among overweight service members in the U.S. Army and Air Force. Future studies should assign exposure using randomization, clarify the mechanism(s) of this relationship, and assess the net balance of harms and benefits of high altitude on obesity prevention.