Background: Since cervical cancer can be prevented and controlled through human papillomavirus (HPV) vaccination, it is important to train health care providers and provide them with appropriate knowledge. This study aimed to understand the level of HPV related knowledge among medical students and correlates in Southwest China in order to address any potential gap in their knowledge base. Methods: We conducted a cross-sectional survey among medical students in six selected universities across Southwest China based on a pretested questionnaire regarding HPV infection, cervical cancer, and HPV vaccines. Results: We successfully surveyed 1, 878 medical students, of whom 32.1% were males and 67.9% were females. Their mean age was 20.8 (standard deviation: 1.3) years. 91.8% of them were ethnic Han Chinese, and 43.8% were students in clinical medicine. While 76.5% had heard of HPV only 48.8% knew that the prevention of cervical cancer was possible through HPV vaccination. Only 42.9% of the male and 49.2% of the female students correctly answered over 10 out of 22 questions on HPV related knowledge. Female students appeared to know more about HPV and HPV vaccination (OR: 1.39; 95% CI: 1.11-1.75). In addition, the student knowledge improved with the grade (p<0.001). University courses were the most selected source of knowledge about HPV vaccination (66.4%). 83.6% of males and 91.4% of females were willing to have more HPV related education by experts (p<0.001). Only 10.1% of the students acknowledged that people had asked for their advice regarding HPV vaccination. Conclusions: Our survey indicates that medical students from Southwest China have poor knowledge of HPV and HPV vaccination, but are willing to receive more relevant information. Targeted education should be incorporated into school courses to inform these future health care providers and ensure success of programs for cervical cancer control and prevention.