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Background There have been some studies of common primary care diseases in Japan, but no reports on which diseases it is difficult for general physicians to diagnose in daily practice. In this study, we identified diseases that provided a diagnostic challenge for Japanese general physicians in daily practice. Methods The subjects were new undiagnosed patients referred to the General Outpatient Department of Chiba University Hospital during the one-year period from January 2008. We performed a retrospective chart review to identify the referring doctor, patient demographics, the duration of symptoms, the final diagnosis, and the outcome. Final diagnoses were classified according to the International Classification of Primary Care Second Edition (ICPC-2). In addition, the differences between referrals from general physicians and those from other physicians were assessed. Fisher's exact test and the Bonferroni-Holm correction were used for statistical analysis. Results A total of 169 patients were referred by general physicians and 239 patients were referred by other physicians. The most common ICPC-2 diagnosis was "General & Unspecified" conditions (35 patients, 20.7%), followed by "Psychological" conditions (31 patients, 18.3%) and "Musculoskeletal" conditions (21 patients, 12.4%). No significant differences of the ICPC-2 category for the final diagnosis and each diagnosis were found between patients referred by general physicians and those referred by other physicians. The hospitalization rate was lower for patients referred by general physicians than for patients referred by other physicians (4 patients, 2.4% vs. 24 patients, 10.0%) (P = 0.002). Conclusions Japanese general physicians found difficulty in diagnosing "Psychological" conditions, "Musculoskeletal" conditions, variations within the normal range, and viral infections that required diagnosis by exclusion. Because most of the patients referred by general physicians had mild conditions, further education at outpatient departments and clinics is required to improve diagnostic performance. Additionally, it is important to increase the gatekeeper role of general physicians and further development of the medical system by the government to distinguish the functions of clinics and hospitals is expected. [ABSTRACT FROM AUTHOR]