The purpose of this study was to see if gender-based differences exist in the performance of dental students at the University of Jordan (UJ), Amman. The retrospective analysis included data from two groups of students: 413 fourth-year dental students (178 males and 275 females) from four consecutive years (2005 through 2008) and 357 fifth-year students (128 males and 229 females) who graduated in the years 2005 to 2008. The influence of gender on the results of the fourth-year students in six theoretical and six clinical courses and the cumulative GPAs of the fifth-year students were studied. In both theoretical and clinical fourth-year courses, multivariate analysis of variance (MANOVA) revealed significant main differences in raw scores between the two gender groups. Female students were significantly better in five theoretical courses. In clinical courses, female students outscored male students in pediatric dentistry and prosthodontics, male students outperformed female students in conservative dentistry and orthodontics, and no significant gender differences were seen in oral surgery and fixed prosthodontics. The cumulative GPAs of the female graduated students were significantly higher than those of the male students. The results showed a significant relationship between gender and academic performance of dental students for these classes. The reasons for these findings should be further investigated.