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Anatomy forms the basis of clinical examination and is integral to today’s medical curriculum. Yet, increasingly evident in the literature is feedback from clinicians and surgeons about the perceived lack of anatomical knowledge among recent medical graduates. To understand the issues surrounding student learning and retention of anatomy, a mixed-methods design was utilized to explore medical students’ anatomical knowledge throughout their Bachelor of Medicine and Bachelor of Surgery (MBBS) degree. Students enrolled in the four-year graduate-entry MBBS course at Monash University participated in the study. Participants from the preclinical (Year A) and clinical years (Years B, C and D) sat an online assessment consisting of 60 clinically relevant anatomy multiple-choice and extended-matched questions whose objectives had been previously covered in the preclinical teaching. Altogether, 136 students participated in the study. The results revealed that knowledge of anatomy declined over time and this was significant in the final two clinical years. The drop in anatomical knowledge was not uniform. The regions of anatomy better retained were associated with frequent exposure and reinforcement in the clinical years. Participants cited an intense and time-constrained curriculum, poor integration in the clinical years and rare opportunities for revising and testing anatomy as reasons for the decline of knowledge. The results of this study highlight the need for conceptual coherence at the time of teaching; the importance of vertical integration in providing students with frequent learning opportunities in the clinical years; and, the value of formatively testing students’ knowledge of anatomy throughout the clinical years.