Hormonal fluctuations during the perimenopausal transition lead to physical discomfort but are also frequently accompanied by mood swings, depressive symptoms, anxiety and sleeping disorders. The important role of the neurotransmitter serotonin in the pathogenesis of anxiety disorders and major depression is unquestioned, but only little is known about the influence of sex hormones on the serotonergic system. This review provides an overview of potential risk factors for the occurrence of affective disorders in the menopausal transition and discusses possible therapeutic options. Current research findings from longitudinal studies testing the efficacy of hormone replacement therapy and antidepressants with effects on the serotonergic neurotransmission on physical and mental discomforts during menopause are presented. Furthermore, studies using positron emission tomography and genetic methods that explore the effects of sex steroids on different components of the serotonergic system are shown. The interactions between estrogen, progesterone and the serotonergic system are described, and possible neurobiological and endocrinological mechanisms underlying depressive symptoms in the perimenopause are elucidated.