Background: Major changes to the teaching of anatomy associated with the integration of basic and clinical sciences in modern medical curricula have coincided with students reporting concern over achievement of learning outcomes in anatomy. Little guidance exists for medical educators designing anatomy courses that account for factors that positively influence medical student confidence in their own anatomy knowledge. We sought to determine what factors are associated with medical students' self-reported confidence in their anatomy knowledge in preparation for clinical practice. Methods: Cross-sectional national survey of Australian medical students distributed using social media. We performed univariate and multivariable ordinal regression to determine the factors in anatomy learning and teaching that influence medical student self-reported confidence to have sufficient anatomy knowledge by the time of graduation, for practice as a junior doctor. Results: Of 1309 surveyed, 1101 (84%) responded, representing 6.5% of the Australian medical student population. Mean age was 23.9 years (SD 4.8 years), a majority were female (644, 58.5%), and students in all years of both undergraduate (52%, 575) and graduate entry courses (48%, 529) were represented. Items associated with increased self-reported confidence in anatomy knowledge included adequate assessment of anatomy (Odds Ratio 2.17 [95% CI 1.69-2.81]), integration of anatomy with other basic sciences (OR 1.97 [1.52-2.56]) and clinical teaching (OR 1.90 [1.46-2.48]), male gender (OR 1.89 [1.48-2.42]), anatomy education prior to medical school (OR 1.46 [1.14-1.87]) and exposure to dissection (OR 1.39 [1.08-1.78]). Medical students in their clinical years reported lower confidence in their anatomy knowledge (OR 0.6 [0.47-0.77], p < 0.0001). Age and career intention were not significant predictors of confidence. Conclusions: Medical educators can enhance student confidence in their own anatomy knowledge by developing curricula that vertically integrating anatomy learning and teaching, integrate anatomy teaching with other basic sciences, and providing consistent assessment through both the pre-clinical and clinical stages of medical training. Anatomy education should also incorporate dissection as a teaching method, and students could benefit from completion of anatomy education prior to medical school. Consideration should also be given to further investigate the confidence of female students in their anatomy knowledge.