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Study Objective The current study presents findings from a qualitative examination of free text comments from a national survey of U.S. physicians on human papillomavirus vaccine recommendation beliefs and practices. Qualitative analyses of free text physician responses may offer a more complete and physician-driven description of influences on human papillomavirus vaccine recommendation. Design and Participants In 2009, a survey assessing physicians' knowledge, attitudes, and human papillomavirus vaccination practices was conducted among a national sample of U.S. physicians practicing Family Medicine, Pediatrics, or Obstetrics/Gynecology (response rate 67.8%). Qualitative comments were analyzed using a Grounded Theory approach. Results Of 1008 completed surveys, 112 participants provided comments, which were organized into three primary HPV vaccine-related themes: (a) comments about cost of the vaccine, (b) comments about institutional policies and procedures, and (c) physicians' personal views and one secondary theme related to survey methodology: the parent study's use of an upfront cash incentive. Many comments pertained to issues that were queried in the closed-end survey items; however, some comments provided insight into understudied areas (e.g., physician attitudes regarding survey methodology). Conclusion Physician respondents used the free text space to reemphasize issues that were most important to them and to offer insight about aspects of the vaccine and the survey process.