Objectives The aim of this work is to assess undergraduate medical student’s opinions on the new trends in medical education course, and to test the effect of medical student’s assessment of medical education course comparing male and female students.

Method Analytical cross-sectional institutional based study conducted at Faculty of Medicine (FMHS), Omdurman Islamic University (OIU), 2018. It was total coverage for all students of first level, therefore, 346 male and female medical students asked to fill pretested questionnaire that contains 9 questions of three domains of knowledge and skills was used to collect the data. The data collected were analyzed using (SPSS) version 20. Frequencies, percentage, Chi-squire were obtained to identify the correlations as analytical statistics between variables of the study. The confidence interval is 95% was taken as significant at P-value ≤ 0.05.

Results There is no statically significant difference between male and female medical students regards assessment of trends in medical education course (P-value > 0.05), in spite they are taught separately. Both male and female students’ assessment revealed positive responds with high percentage in cognitive knowledge, psychomotor and behavioral skills that studied in the course.

Conclusions Almost all students were ensured their agreement particularly in Self-learning, Small Group Work and Problem Based Learning (PBL) in the course.

In conclusion, no statistical difference between male and female medical students’ assessment of trends in medical education course in this study.