Computer visualizations are increasingly common in education across a range of subject disciplines, including anatomy. Despite optimism about their educational potential, students sometime have difficulty learning from these visualizations. The purpose of this study was to explore a range of factors that influence spatial anatomy comprehension before and after instruction with different computer visualizations. Three major factors were considered: (1) visualization ability (VZ) of learners, (2) dynamism of the visual display, and (3) interactivity of the system. Participants (N = 60) of differing VZs (high, low) studied a group of anatomical structures in one of three visual conditions (control, static, dynamic) and one of two interactive conditions (interactive, non-interactive). Before and after the study phase, participants' comprehension of spatial anatomical information was assessed using a multiple-choice spatial anatomy task (SAT) involving the mental rotation of the anatomical structures, identification of the structures in 2D cross-sections, and localization of planes corresponding to given cross-sections. Results indicate that VZ had a positive influence on SAT performance but instruction with different computer visualizations could modulate the effect of VZ on task performance.