BACKGROUND: The prevalence of complementary and alternative medicine (CAM) use has been estimated to be as high as 65% in some populations. However, there has been little objective research into the possible risks or benefits of unmanaged CAM therapies. METHODS: In this prospective study of active duty US Navy and Marine Corps personnel, the association between self-reported practitioner-assisted or self-administered CAM use and future hospitalization was investigated. Cox regression models were used to examine risk of hospitalization due to any cause over the follow-up period from date of questionnaire submission, until hospitalization, separation from the military, or end of observation period (June 30, 2004), whichever occurred first. RESULTS: After adjusting for baseline health, baseline trust and satisfaction with conventional medicine, and demographic characteristics, those who reported self-administering two or more CAM therapies were significantly less likely to be hospitalized for any cause when compared with those who did not self-administer CAM (HR = 0.38; 95% CI = 0.17, 0.86). Use of multiple practitioner-assisted CAM was not associated with a significant decrease or increase of risk for future hospitalization (HR = 1.86; 95 percent confidence interval = 0.96-3.63). CONCLUSION: While there were limitations to these analyses, this investigation utilized an objective measure of health to investigate the potential health effects of CAM therapies and found a modest reduction in the overall risk of hospitalization associated with self-administration of two or more CAM therapies. In contrast, use of practitioner-assisted CAM was not associated with a protective effect.