BACKGROUND: The general medicine in-training examination (GM-ITE) is designed to objectively evaluate the postgraduate clinical competencies (PGY) 1 and 2 residents in Japan. Although the total GM-ITE scores tended to be lower in PGY-1 and PGY-2 residents in university hospitals than those in community-based hospitals, the most divergent areas of essential clinical competencies have not yet been revealed. METHODS: We conducted a nationwide, multicenter, cross-sectional study in Japan, using the GM-ITE to compare university and community-based hospitals in the four areas of basic clinical knowledge". Specifically, "medical interview and professionalism," "symptomatology and clinical reasoning," "physical examination and clinical procedures," and "disease knowledge" were assessed. RESULTS: We found no significant difference in "medical interview and professionalism" scores between the community-based and university hospital residents. However, significant differences were found in the remaining three areas. A 1.28-point difference (95% confidence interval: 0.96-1.59) in "physical examination and clinical procedures" in PGY-1 residents was found; this area alone accounts for approximately half of the difference in total score. CONCLUSIONS: The standardization of junior residency programs and the general clinical education programs in Japan should be promoted and will improve the overall training that our residents receive. This is especially needed in categories where university hospitals have low scores, such as "physical examination and clinical procedures."