Human papillomavirus (HPV) is the most common sexually transmitted infection among U.S. military members. The most frequent clinical manifestation of HPV is genital warts (GW). This investigation examined the annual incidence of diagnoses of GW among U.S. service members before and after the availability of the quadrivalent HPV (HPV4) vaccine in 2006. Incidence rates of GW diagnoses markedly declined among female service members in the HPV4 vaccine-eligible age range from 2007 (following introduction of the HPV4 vaccine) through 2010. In contrast, among women 25 years and older and men of all age groups, annual rates of GW diagnoses remained relatively low and stable from 2000 through 2010. The higher rates of diagnoses of GWs among female than male service members reflect the effects of routine periodic gynecologic screening. Slight increases in the incidence of GW diagnoses among men between 2010 and 2012 may in part reflect the repeal of the U.S. military's "Don't Ask Don't Tell" policy.