Background: Recurrent headaches are disqualifying for military service if they are of sufficient severity or frequency to interfere with normal function in the past 3 years. The occupational impact of waiving this standard is evaluated. Methods: A retrospective cohort study of enlistees from January 1, 1995, through December 31, 2000, was performed. Enlistees with a waiver for recurrent headaches were compared with fully qualified enlistees (matched 3:1) for retention in the military, headache-related discharges, and hospitalizations. Results: The 174 individuals with waivers for a history of recurrent headaches were retained on active duty at the same rate as the 522 matched control subjects (log rank test, p = 0.91). Medical record review of waivers documented no debilitating headaches within 1 year before the medical examination. Conclusions: These results validate the current headache waiver criteria from the perspective of retention and suggest a more lenient medical accession standard. Future studies should evaluate the morbidity and occupational impact of headaches in the U.S. military.