National guidelines recommend human papillomavirus (HPV) vaccination for all 11-12-year-olds, but uptake among United States adolescents remains low. A major barrier to greater uptake is the lack of effective recommendations for HPV vaccine from clinicians. One potential influence on clinicians' recommendations for HPV vaccine that has been relatively unexplored is that of cognitive biases, or errors in judgement that result from 'mental shortcuts' used to make decisions under uncertainty. Therefore, we analyzed qualitative data from interviews with 32 pediatric clinicians using a framework of nine cognitive biases relevant to HPV vaccination: omission bias, ambiguity aversion, present bias, availability bias, optimism bias, naturalness bias, protected values, anchoring bias, and confirmation bias. We used a directed content analysis approach to iteratively code and analyze all transcripts in the dataset. We found evidence for several cognitive biases that were related to weaker recommendations for HPV vaccine. Commonly identified biases included anchoring bias (perception that vaccination unnecessary due to age/pubertal status); present bias (perception of burdens related to discussing vaccination), and optimism bias (belief that patient at low risk for HPV acquisition). We found less frequent evidence for ambiguity aversion (perception of missing information regarding vaccination) and omission bias (deferring vaccination). Other biases were identified infrequently or not at all. Our findings suggest that several cognitive biases may be an influence on clinicians' communication about HPV vaccine. Raising awareness of cognitive biases related to making HPV vaccine recommendations could help to strengthen the recommendations that clinicians provide.