Study Objective Many adolescents with chronic medical conditions (CMCs) are at risk of HPV infection, associated complications, and under-immunization and often identify a pediatric subspecialist as their main provider. This study aimed to assess the HPV-related understanding, beliefs, and practices of pediatric subspecialists, which are largely unknown. Design and Setting National cross-sectional study. Participants Pediatric endocrinologists, hematologist/oncologists, pulmonologists, and rheumatologists identified using the American Medical Association Physician Masterfile. Interventions Subspecialists caring for adolescents with CMCs in the outpatient setting were recruited to complete a web-based survey examining their HPV-related knowledge, attitudes, comfort, and practices. Main Outcome Measures HPV vaccination recommendation. Results Of respondents (n=418), 50.4% reported sometimes or always recommending HPV vaccination to adolescent patients with CMCs. Factors positively associated with recommendation included hematology/oncology (AOR 4.69, 95% CI 1.86–11.81) or rheumatology (AOR 6.55, 95% CI 1.67–25.74) specialization, seeing more adolescent patients with CMCs (AOR 1.01, 95% CI 1.00–1.02), and sometimes or always discussing sexual health (AOR 2.53, 95% CI 1.05–6.08) or checking vaccine status (AOR 3.83, 95% CI 1.59–9.20) with these patients. Those who thought it was important, but were uncomfortable discussing sexual health when recommending HPV vaccination (AOR 0.28, 95% CI 0.12–0.70) or who reported insufficient HPV vaccine information (AOR 0.45, 95% CI 0.23–0.88) or lack of primary-subspecialty care provider communication (AOR 0.38, 95% CI 0.16–0.93) as barriers to HPV vaccination were less likely to recommend HPV vaccination. Conclusions This study reveals that many subspecialists fail to recommend HPV vaccination to adolescents with CMCs and highlights potential targets for future interventions.