Background: Human Papillomavirus (HPV) is the most common sexually transmitted infection (STI) among soldiers in the US Army. This study examines compliance patterns of female soldiers who receive the HPV prevention vaccine Gardasil in a Military Treatment Facility. Methods: Medical records of all female Soldiers aged 18 to 26 registered at Womack Army Medical Center (n = 3,186) were examined retrospectively. Patients identified with a Current Procedural Terminology (CPT) 90649, Human Papillomavirus (HPV) vaccine code encounter were included. Data were collected for all patients between November 1, 2006 and December 15, 2009. Results: Approximately 15% received Gardasil; of these only 37% completed the required 3-dose series. Conclusions: A number of recommendations to increase initiation of the vaccine series are suggested. Steps should also be taken to educate providers in using required annual physicals to start a discussion of the vaccine and to administer the first dose. To increase the visibility of the vaccine, this education could be completed at educational lectures, at residency lectures or at staff meetings within clinic areas. This study is intended to remind providers to initiate the HPV vaccine series and the importance of completing the entire series in all eligible females.