To explore the association between the knowledge of basic (physiology and biochemistry) and clinical sciences (internal medicine) among medical students, and determine the level of retained basic science knowledge at the fifth year of medical studies.Medical students attending the second (n=145, response rate 60%) or the fifth year (n=176, response rate 73%) of medical studies at the Zagreb University School of Medicine in Croatia were given an anonymous knowledge test with 15 pairs of questions developed specifically for this purpose. Each pair consisted of a basic and clinical question, with the correct answer to the basic question explaining the physiological or biochemical background of the clinical question. Three pairs of questions were excludes from the analysis due to poor psychometric characteristics.We found statistically significant correlation between basic and clinical tests scores for both groups of students (r=0.47, P<0.001 for the second year and r=0.45, P<0.001 for the fifth year). 2x2 within-between measures ANOVA revealed a significant interaction effect for knowledge test and study year (Wilks lambda=0.55, F(1, 319)=262.7, P<0.001; effect size=0.45), showing that fifth year students scored lower on the basic test than second year students but obtained higher scores on the clinical test.The core basic science knowledge is lost during the clinical years of medical studies. Although remembering and understanding basic science concepts as a background of clinical statements at the clinical years does not directly affect clinical knowledge, there is a positive correlation between retained basic science concepts and clinical knowledge.