The Department of Anatomy at the University of Otago offers anatomical sciences education for various programs, but currently, little information is available on how the academic performance of anatomy students differ based on ethnicities. Here, we aim to determine if there is an ethnic disparity in academic performance among anatomy students at the University of Otago. We conducted a 5-year review of academic performance of New Zealand European (NZE) and Pasifika students in 10 undergraduate anatomy courses, including clinical anatomy, neuroscience, reproduction, cell biology, and biological anthropology. NZE students achieved higher marks than Pasifika students in each academic year for four courses and in 3-4 of 5 academic years for the remaining courses. In eight courses, there were higher proportions of Pasifika students than NZE students who repeated the courses (in 4-5 of 5 academic years for two courses, in 1-2 of 5 academic years for six courses). Multiple regression analyses showed that Pasifika students were more likely to achieve lower marks than NZE students in all courses. Other predictors for academic marks included year of study for five courses, age for three courses, international student status for two courses, major specialization for eight courses, home location for one course, and gender for one course. Data from this research provide evidence that ethnic inequity may exist in anatomical sciences education, and can be used by institutions globally to justify evaluating their anatomy programs, with the aim to better support ethnic minority students who may be struggling academically.