Purpose: Spatial perception is an essential skill for professional dentists. The objective of this study was to observe the spatial ability, as well as anatomy module grades, of dental students at a dental education center in Indonesia and relate these to gender and cohort. Methods: A cross-sectional study was carried out where dental students in years (cohorts) 1, 2, 4–6 were invited to take the Revised Purdue Spatial Visualization Test (PSVT-R) and the redrawn Vandenberg and Kuse Mental Rotation Test (MRT) in order to assess spatial ability. In addition, the 1st- and 2nd-year dental students carried out gross anatomy assessments. Spatial ability test results were compared using an independent t-test to detect gender differences, one-way analysis of variance to inspect cohort differences, and correlation relative to anatomy module scores. Results: A total of 326 dental students voluntarily participated. Statistically significant gender differences were found in both spatial ability tests in the overall sample (PSVT-R: p<0.001; MRT: p=0.001). When the 1st- and 2nd-year dental students were pooled, significant gender differences were detected, in which males scored higher than females in both spatial ability tests (PSVT-R: p<0.001; MRT: p=0.003). In anatomy, however, females scored higher than the males (p=0.005). In addition, there were weak to moderate, but significant correlations between spatial ability tests and anatomy scores. Conclusion This study indicated that spatial ability may not be the only factor predicting the academic performance of dental students. However, dental students with low spatial ability scores may need supplementary educational techniques when learning specific spatial tasks.