The purpose of this study was to assess middle-aged Japanese workers for possible gender differences in the risk factors associated with depressive symptoms and suicidal ideation. 5,878 workers (40–60 yr of age) (3,631 males and 2,247 females) were recruited from randomly selected companies in northern Japan. Demographic and lifestyle factors, suicidal ideation rate, and the data for the Brief Job Stress Questionnaire (BJSQ) and the Center for Epidemiologic Studies for Depression scale (CES-D) were obtained from the self-report questionnaires. After adjusting for possible confounding variables, marital status, absent of stress reduction technique and low job compatibility were significant independent risk factors for suicidal ideation among males. In females, marital status, feeling of insufficient sleep and absence of stress reduction techniques were significant independent risk factors after adjusting for all variables. Under the same adjustments, temporary employment also showed a protective effect against female suicidal ideation. In conclusion, our results suggest that factors related to suicidal ideation differed by gender. Different approaches for each gender might be useful in the development of suicide prevention programs. However, interpretation of work-related effects, such as temporary employment, interpersonal conflict and transportation industry, was hampered by lack of data concerning personal income, working hours and organizational commitment. Additional studies are needed to examine the longitudinal relationships between the risk factors associated with suicidal ideation and depressive symptoms.