Military training exercises are conducted routinely in the Mojave Desert. To determine whether assignment in this desert environment increases risk of respiratory illnesses, hospitalization rates were compared between two matched cohorts of soldiers during three intervals of follow-up during a 10-year surveillance period. The exposed cohort (N = 21,543) included all soldiers who were ever assigned to the Mojave Desert during the surveillance period. The control cohort (N = 86,172) included soldiers matched on demographic characteristics who were never assigned to the Mojave Desert during the surveillance period. Three follow-up intervals ("before," "during," "after") were defined relative to times when exposed soldiers were assigned to the desert. Rates of respiratory hospitalizations were similar between the cohorts for the "before" and "during" intervals but were higher in the exposed cohort for the "after" interval (rate ratio, 1.30; 95% confidence interval, 1.07-1.59). This difference was largely attributable to excess pneumonia and influenza hospitalizations in the exposed cohort. Healthy, young adults may have increased susceptibility to respiratory infectious illnesses after prolonged exposures to desert environments.