In modern curricula, the early integration of anatomy and clinical skills education at undergraduate level is seen as important. However, the direct relationship between medical students' competence in anatomy, and their clinical proficiency during early undergraduate years, has scarcely been studied. In this study, the marks for anatomy and clinical skills of three consecutive cohorts of medical students (n = 538 in total) during their first two years were correlated. The anatomy competence was measured using a new marker, the Anatomy Competence Score (ACS) which was calculated with equal contributions from theory knowledge and its practical and clinical application. Proficiency in clinical skills was determined by OSCE performance marks for stations which examined physical examination and practical procedural skills. The possible compounding effect of students' general academic ability was investigated by using the overall performance mark for each student based on their performance in all subjects over the first two years of the medical curriculum. We found that the correlation between anatomy and clinical skills marks was weak to moderate. However, this correlation was virtually nullified once the effect of academic ability was accounted for. Although these findings suggest that anatomy education does not compliment early clinical education, the lack of complexity of clinical problems used in clinical skills assessments (OSCEs) during the early stages may well be the primary contributing factor to this finding.