Introduction: Sexual health education is paramount in curbing the rising numbers of sexual transmitted diseases in Malaysia. Medical undergraduates which are the future frontier play an utmost role in educating and quell the social barrier in discussion on this taboo topic. We aimed to determine the knowledge, perception and factors affecting sexual health education among medical students in MMMC and to advocate sexual health education at primary level. Methods: A cross-sectional study was conducted among 309 respondents comprises of Year 3, 4 and 5. Results: There was significant association between age, gender, religion and ethnicity and sexual health knowledge and perception score. Pearson correlation coefficient shows there was positive correlation (r = 0.059) between total sexual health knowledge percentage score and total perception score but was not significant. Conclusion: Medical undergraduates should improve their knowledge and perception regarding sexual health education. It is recommended to implement sexual education in high school curriculum and institution of higher learning in Malaysia as it is not implemented yet here due to political and religion sensitivity. It is also important that students develop personalities that are ready to accept exchange and contribute sensitive issues such as sexual health.