In this chapter, we address biological molecules and systems found to be associated with perinatal mental health, including genetics and epigenetics, neurotransmitter systems, the endocrine system, the immune system, growth factors, vitamins, minerals, oxidative stress parameters, the microbiome, and the metabolome. Mental health disorders in the perinatal period include a broad spectrum of diseases such as depression, anxiety, psychosis, posttraumatic stress, obsessive-compulsive disorder, fear of childbirth, and eating disorders. We focus mainly on perinatal depression and complement it with related knowledge of other mental disorders in the perinatal period.