In recent years increased interest in the connection of intestinal microflora and the state of human health resulted in a great deal of research on the influence of intestinal microflora in particular on mental health, including works on affective functions of the central nervous system (CNS). Previous studies on animals have revealed the existence of a bi-directional communication system between the gastrointestinal microbiota and the central nervous system, the so-called .gut–brain axis’ which modulates functioning of CNS through immunological, endocrine and neuronal mechanisms. Clinical studies have shown a connection between supplementation of probiotics containing specific species and strains of bacteria and the regulation of the body’s response to stress and with the exacerbation of depressive and anxiety symptoms in humans. Studies have also demonstrated differences in the composition of the intestinal microflora of patients with a diagnosis of major depressive disorder in comparison with the healthy population. The aim of this article is to present the current state of knowledge on the relationship between composition of intestinal microflora and affective functions of CNS and on effects of supplementation of probiotics on depressive and anxiety symptoms in humans. Previous studies on the use of probiotics in the prophylaxis and treatment of depressive and anxiety disorders included too small groups of persons, especially in groups of patients diagnosed with depression, to be able to clearly determine the effectiveness of probiotics in prevention and, in particular, treatment of these disorders in humans.