We reviewed clinical and billing data from a university-based health system to assess HPV vaccine utilization among 9-18-year-old girls by individual, visit and medical specialty characteristics. Our sample included 10,082 adolescent patients with 27,928 visits to outpatient family medicine (FM), pediatric and gynecology clinics between January 2007 and March 2008. Vaccine series completion was low among eligible adolescents (15%), with important disparities in vaccine utilization by medical specialty, age, race and insurance status. Missed opportunities for vaccination were common. Our findings may help to target future interventions aimed at increasing adolescent HPV vaccine utilization.