Background: There is no clear association between menopause and depression. Aim of the study was to compare female depression with onset before menopause with female depression with onset after menopause, to find out if endocrinological changes had an impact on depression. Methods: Five hundred and twelve consecutive unipolar and bipolar I/II depressed outpatients were interviewed with the Structured Clinical Interview for DSM-IV, the Montgomery-Asberg Depression Rating Scale and the Global Assessment of Functioning scale. Patients were divided into patients with depression/mania onset before 40 and after 40. Results: Female depression with onset after 40 had a significantly shorter duration of illness, fewer recurrences, fewer patients with atypical features, fewer bipolar II patients and more unipolar patients than female depression with onset before 40. Male depression with onset after 40 had a significantly shorter duration of illness and fewer patients with atypical features than male depression with onset before 40. Conclusions: Some features were common to both female and male depression with onset after 40. Female depression with onset after 40 had significantly more unipolar and fewer bipolar II patients, than female depression with onset before 40. Different frequency of unipolar and bipolar II patients suggests that the biology of depression in menopause women may be different from that of women not in menopause, and from that of male depression with onset after 40. Differences may be related to menopause.