Objective: In many Japanese medical schools, pass rates of males were higher than those of females although in Japan there are already fewer female candidates for medical schools in comparison with Western countries. Thus, we investigated some factors that cause an inordinately large effect on lower female success rates or higher female enrolment ratios for medical schools, from public medical schools by multiple regression analysis. Methods: A multiple regression analysis was conducted on the two dependent variables, female success ratio and female enrolment ratio. Explanatory variables included the weightage of the second exam; the value given to maths and science subjects; the quotas for the second intake; the ranking of the medical school; the year of establishment of the medical school; and the population of the city where the medical school is located. Results: Increased weightage accorded to maths and science subjects caused significantly severe difficulties in the candidature of female candidates. Furthermore, medical schools with significantly higher female enrolment ratios were relatively new. Conclusion: These results represent the backwardness of Japan in gender equality. To mitigate this situation, the entrance examination process of medical schools must first be reformed.