OBJECTIVE Stigma associated with behavioral health problems in the military pose challenges to accurate base rate estimations. Recent work has highlighted the importance of anonymous assessment methods, yet no study to date has assessed the ability of anonymous self-report measures to mitigate the impact of stigma on honest reporting. This study used the unmatched count technique (UCT), a form of randomized response techniques, to gain information about the accuracy of base rate estimates of alcohol misuse derived via anonymous assessment of Operation Enduring Freedom/Operation Iraqi Freedom active duty service members. METHOD A cross-sectional, convenience sample of 184 active-duty service members, recruited via online websites for military populations, provided data on two facets of alcohol misuse (drinking more than intended and feeling the need to reduce use) via traditional self-report and the UCT. RESULTS The UCT revealed significantly higher rates relative to traditional anonymous assessment for both drinking more than intended (51.9% vs. 23.4%) and feeling the need to reduce use (39.3% vs. 18.2%). CONCLUSIONS These data suggest that anonymity does not completely mitigate the impact of stigma on endorsing behavioral health concerns in the military. Our results, although preliminary, suggest that published rates of alcohol misuse in the military may underestimate the true rates of these concerns. The UCT has significant potential to improve base rate estimation of sensitive behaviors in the military.