Anatomy as an indispensable part of the medical curricula, offering impeccable knowledge, prepares the students to enter the practical atmosphere. The aim of this study was to evaluate the clinical application of anatomy courses of the medical students in Zanjan University of Medical Sciences. This cross-sectional study was conducted in 2015 with census sampling on all clinical students (trainees and interns). To collect feedback from students, the questionnaire designed by researchers was used. The Likert rating scale of very high, high, medium, low, and very low was considered and scores of 5 (very high) to 1 (very low) were applied. Data were analyzed by SPSS software. Among the courses of anatomy, trunk anatomy has the greatest impact on clinical courses of medical students (P<0.001). Subjects of muscular system, lymphatic system, vascular system, and nervous system were of significant clinical application during clinical periods; however, no significant clinical application observed for skeletal system (P<0.05). Teaching clinical tips by professors can help improve the performance of medical students in clinical education. In addition, using three-dimensional anatomical software is suggested as well.