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The number of women physicians is increasing in Japan. The authors investigated gender differences in self-perceptions of clinical confidence.This cross-sectional study was conducted in March 2007 by using a stratified random sample of 1,124 second-year resident physicians. Residents' confidence levels were assessed, using four-point Likert scales (e.g., 1 for “not at all” to 4 for “very much”), in four competency sets: physical exams, procedural skills, interpretations of clinical tests, and physician–patient relationships and social service application. Gender effect was investigated for clinical confidence levels by general linear models adjusting for age, types of hospitals, number of clinical experiences, satisfaction with residency conditions, future career, and perspectives on life and work.The overall mean confidence scores in the four sets ranged between 2.9 and 3.1. Compared with men, women were younger (P = .001), more likely to be oriented more to life than to work (P < .001), less interested in doctor of medical science degrees (P = .001), and less likely to be satisfied with residency conditions (P = .020). A significantly greater proportion of women chose “family” (70% versus 54% for men) as “the most important thing in life.” Compared with men, women were less confident in the majority of competency areas even after adjusting for the number of clinical experiences.This nationwide resident survey demonstrated gender differences in clinical confidence levels. Future studies require careful monitoring of self-confidence and its impact on physicians' professional development.