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Health literacy is important in public health and healthcare, particularly in effective communication between patients and health professionals. Although most medical students will eventually work as health professionals after graduation, research on health literacy of medical students is scarce. This study aimed to assess the health literacy level of medical students in Chongqing, China, and its influencing factors. A cross-sectional study was conducted and 1,275 participants (250 males and 1,022 females) who majored in five different disciplines were involved. The Health Literacy Questionnaire was used as the survey tool. The junior students obtained the highest scores, whereas the freshman students had the lowest scores on each scale. The average score of males was higher than that of females except in “feeling understood and supported by healthcare providers,” and the average score of students who reside in urban areas was higher than that of students in rural areas. Moreover, the average score of engineering students was higher than that of medical or health sciences students. Multiple linear regression models (Radj2 = 0.435, P = 0.000) showed that the grade, socioeconomic status, and parent’s highest level of education were positively correlated with health literacy. In conclusion, the health literacy levels of the medical students are insufficient and need improvement. [ABSTRACT FROM AUTHOR]