Students' motivation is a vital determinant of academic performance that is influenced by the learning environment. This study aimed to assess and analyze the motivation subscales between different cohorts (chiropractic, dental, medical) of anatomy students (n = 251) and to investigate if these subscales had an effect on the students' anatomy performance. A 31-item survey, the Motivated Strategies for Learning Questionnaire was utilized, covering items on intrinsic and extrinsic goal orientation, task value, control of learning belief, self-efficiency for learning and performance, and test anxiety. First-year dental students were significantly more anxious than chiropractic students. Second-year chiropractic students attached more value to anatomy education than second-year medical students. The outcome of this research demonstrated a significant relationship in first- and second-year chiropractic students between anatomy performance and motivation subscales controlling for gender such as self-efficacy for learning and performance was (β= 8 CI: 5.18 - 10.8, P < 0.001) and (β = 6.25,CI: 3.40 - 9.10, P < 0.001) for first-year and second-year respectively. With regards to intrinsic goal orientation, it was (β = 4.02, CI: 1.19 - 6.86, P = 0.006) and (β = 5.38, CI: 2.32 - 8.44, P = 0.001) for first-year and second-year respectively. For the control of learning beliefs, it was (β = 3.71, 95% CI: 0.18 - 7.25, P = 0.04) and (β = 3.07, CI: 0.03 - 6.12, P = 0.048) for first-year and second-year respectively. Interventions aimed at improving these motivation subscales in students could boost their anatomy performance.