What is the influence of psychotherapy over the brain functioning? Is it possible for us to determine in which type of psychotherapy the most significant changes in the brain functioning are observed? If the influence of psychotherapy over the brain is a fact, does this fundamentally change the training in psychology, psychiatry and psychotherapy and the inclusion of knowledge from the basic sciences? Psychotherapy can be considered as a type of training that stimulates the patient to learn how to change their behaviour, thinking and regulation of emotions. Psychotherapy is much more than an opportunity to talk to someone with good listening skills. Understanding the relationship between psychotherapy and brain functions is stimulating news and changes the traditional thinking about the place of psychotherapy and pharmacotherapy, the relations between them in the process of overcoming mental problems and diseases. Psychotherapy is assumed to be a form of learning which suggests that the uptake of information in the process of psychotherapy leads to a change in the expression of genes, thus changing the strength of synaptic connections. The gene sequence does not change under the influence of the environment, but the ability of genes to direct the synthesis of individual proteins depends on environmental factors and is regulated by their influence (Candel,1998). This explains the phenotypic differences between monozygotic twins and discordance of diseases, such as schizophrenia. Any mental condition is a brain state and any mental disorder is a disorder in the work of the brain. The effect of treatment of mental disorders is associated with an effect on structural and functional changes in the brain (Candel,1998). Neuroimaging gives an objective diagnostics of mental disorders, revealing the reasons for their occurrence and therefore allows for the development of more effective methods of treatment and psychotherapy.