The 12-item General Health Questionnaire (GHQ-12) has been extensively used in a variety of settings across countries. The main aim of the present study was to assess the factor structure of the GHQ-12 for the Japanese general adult population. Data came from a sample of 1808 Japanese aged 20 years or older who were randomly selected based on the 1995 census (897 men and 911 women). Cronbach's alpha coefficients were 0.83 for men and 0.85 for women. Overall, the corrected item-total correlation coefficients were >0.20 for both genders. The GHQ-12 yielded a two-factor solution of psychological distress (items 2, 5, 6, 9, 10 and 11) and social dysfunction (items 1, 3, 4, 7 and 8), which jointly accounted for 49.1% of the total variance, for women. Item 12 on happiness was not discernable. For men, item 12 was separated from a social dysfunction factor and yielded the third factor with item 3 on social role, and the three factors jointly accounted for 57.6%. The results of the present study suggest that the GHQ-12 can be used as an internally reliable and homogeneous scale that produces mainly the factors of psychological distress and social dysfunction. Item 12 may be structurally different in the case of Japanese adults.