Background: Increasing rates of coccidioidomycosis among the general population are being described. Given the large number of military personnel stationed and training in endemic areas, data regarding infection trends among military members would be informative. Methods: We performed a retrospective epidemiological study concerning the incidence and severity of clinical cases of coccidioidomycosis at a naval base located in an endemic area in California. Results: Eighty-two military beneficiaries at the base were diagnosed with coccidioidomycosis from January 2002 to December 2006. Among active duty personnel, the rate of coccidioidomycosis rose 10-fold during the 5-year study period: 29.88 to 313.71 cases per 100,000 person-years. The incidence of coccidioidal infections occurring in active duty members was higher than other military beneficiaries at the base. The median age of patients with a coccidioidal infection was 28 years, and 73% were male. Sixty-six had primary pulmonary disease and 14 had disseminated disease; data were unavailable for two cases. The number of disseminated cases increased significantly over time; by 2006, 30% of the diagnosed cases were disseminated disease. Among cases of dissemination, 43% occurred among Caucasian/non-Hispanics. Disseminated disease was associated with high complement fixation titers and a more recent year of diagnosis. Although the sample size was small, we found no differences in rates of disseminated disease by race, likely due to the large number of cases among Caucasians. Conclusions: Coccidioidomycosis incidence rates have significantly increased during the last 5 years among military beneficiaries. Active duty members were more likely to develop coccidioidomycosis than dependents or retirees, perhaps related to the number and intensity of exposures in this group.