Objective: To assess postgraduate candidates’ knowledge on basic sciences and to compare their achievement based on two years study in the Department of Psychiatry, National University of Malaysia (UKM), Kuala Lumpur, Malaysia. Methods: This is a study assessing areas of difficulties in basic sciences for the Malaysian postgraduate candidates sitting for mock MCQ examination papers in two consecutive years. Results: The candidates in both years failed on MCQ papers (scoring marks are only 43% and 40% for the year 2006 and 2005 respectively), which is consistent with their final examination outcomes. The candidates in the year 2006 were much superior in neuroanatomy (percentages of median scores: 47% vs. 31%, p<0.05), neurophysiology (54% vs. 47%, p<0.05) and psychology (44% vs. 41%, p<0.05) domains compared to their counterparts taking examination in the year 2005. However, there was no difference in terms of other domains, such as neurochemistry, psychopathology and epidemiology in the examination outcomes for the year 2005 and 2006. Generally, the overall scores of the candidates participating in the year 2006 were much higher than their previous counterparts. However, the scores of the candidates of both years were still low in statistics (34.1% vs. 36.4%, p >0.05) and stress/immunology (38.2% vs. 37.3%, p>0.05). Conclusion: Medical statistics and stress/immunology remain difficult subjects compared to neurophysiology and psychopharmacology. Malaysian postgraduate candidates need more efforts to understand basic sciences, especially statistics.