Background: Anatomy is a foundational component of medical education. However, many students find it challenging to apply anatomical knowledge in clinical problem-solving. Understanding their ability to interpret clinical scenarios during the pre-clinical phase can help identify educational gaps. This study evaluated the ability of undergraduate medical students to answer clinically oriented multiple-choice questions (MCQs) compared with non-clinical ones in regional anatomy, and compared performances between first- and second-year students. Methods: A cross-sectional analytical study was conducted among 220 Phase-I MBBS students (110 first-year and 110 second-year) in a government medical college in Dhaka, Bangladesh, from July 2022 to June 2023. Students were randomly assigned into clinical and non-clinical groups (n=55 each per year). Two validated sets of 10 MCQs were prepared from Snell’s Clinical Anatomy by Regions (10th edition), reflecting either clinically applied or descriptive content. Scores for correct, incorrect, and unattempted responses were compared using independent sample t-tests in SPSS version 25. Results: Non-clinical groups in both years achieved significantly higher mean scores than clinical groups (p<0.001). First-year non-clinical students scored 45.45±1.84 versus 37.02±2.95 in the clinical group, while second-year non-clinical students scored 42.89±2.84 versus 37.11±1.88 in the clinical group. Differences between first- and second-year clinical groups were not significant, but first-year non-clinical students performed slightly better than their second-year counterparts (p<0.05). Conclusion: Students demonstrated stronger factual knowledge than applied understanding. Early incorporation of clinical relevance in anatomy teaching, supported by case-based and interdisciplinary approaches, is recommended to enhance clinical reasoning.