OBJECTIVE We investigated gender differences in bipolar disorder (BD) type I and II in a representative cohort of secondary care psychiatric in- and out-patients. METHODS In the prospective, naturalistic Jorvi Bipolar Study of 191 secondary care psychiatric in- and out-patients, 160 patients (85.1%) could be followed up for 18 months with a life chart. RESULTS After adjusting for confounders, no marked differences in illness-related characteristics were found. However, female patients with BD had more lifetime comorbid eating disorders (P < 0.001, OR = 5.99, 95% CI 2.12-16.93) but less substance use disorders (P < 0.001, OR = 0.29, 95% CI 0.16-0.56) than males. Median time to recurrence after remission was 3.1 months longer among men than women, female gender carrying a higher hazard of recurrence (P = 0.006, HR = 2.00, 95% CI 1.22-3.27). CONCLUSIONS Men and women with type I and II BD have fairly similar illness-related clinical characteristics, but their profile of comorbid disorders may differ significantly, particularly regarding substance use and eating disorders. In medium-term follow-up, females appear to have a higher hazard of recurrence than males.