Introduction: Measuring students’ perception of anatomy education environment provides important information for quality assurance and improvement in anatomy education. This study evaluated medical students’ perception of anatomy education environment in Universiti Putra Malaysia by using a validated tool, the Anatomy Education Environment Measurement Inventory (AEEMI). Methods: A cross-sectional study was conducted in the Faculty of Medicine and Health Sciences, Universiti Putra Malaysia between August and September 2020. Stratified random sampling was used to ensure balance sampling of two sociodemographic parameters: gender and study phase. The AEEMI was distributed online to 384 consenting students who rate their perceptions on the six factors of AEEMI: anatomy teachers and instructor, importance of anatomy knowledge, intrinsic interest in learning anatomy, anatomy learning resources, students’ effort to learn anatomy and quality of histology learning facilities, using a five-point Likert scale. The average score of each factor was calculated and compared between male and female respondents, and between preclinical and clinical ones, using SPSS version 25. Results: All factors was rated to be positive with scores > 4.00, except for histology practical facilities that was perceived as an area for improvement (score 3 – 4.99). There was no significant difference of the scores between male and female respondents, and between preclinical and clinical ones. The scores were found to be consistent across gender and study phase. Conclusion: Anatomy education environment in UPM are positive and caters for the differences in gender and study phase. Nevertheless, the histology practical facilities may require further attention for improvement.