Purpose: Human papillomavirus (HPV) vaccination uptake continues to be low in the United States. While a recommendation from a health care provider (HCP) has been shown to be associated with vaccine acceptability among parents, little is known about factors associated with hesitancy despite HCP recommendation. We examined factors associated with HPV vaccine hesitancy, despite a physician recommendation, among Latina immigrant mothers of daughters aged 9-12 years. Methods: As part of a group randomized trial to promote HPV vaccination between 2013 and 2016, we conducted a baseline interviewer-administered survey of mothers to assess sociodemographics, knowledge and perceived risk of cervical cancer/HPV infection, self-efficacy, and intention to vaccinate their unvaccinated daughters. Hesitancy was defined as “don’t know/not sure” (DK/NS) in response to the question: “If your daughter’s doctor recommended that she gets the HPV vaccine, would you let her get it?” Results: Of the 317 participants, 35.3% indicated hesitancy to vaccinate their daughters if their physician recommended it. Although a number of variables were associated with HPV vaccine hesitancy in the univariate model, five remained significant in the final multivariable model: daughter’s health insurance status; HPV awareness; perceived risk of HPV infection for their daughters; perceived self-risk of cervical cancer; and a self-efficacy score of ability to complete the HPV vaccination series. Conclusions: A recommendation by a health care provider may be not enough to motivate Latina immigrant mothers to vaccinate their daughters. Further efforts should focus on increasing awareness regarding HPV and cervical cancer, heightening perceived risk of HPV infection among daughters and boosting self-efficacy to get their children vaccinated against HPV.