SUMMARY Since the time of Freud’s “Project for psychology as natural science” in 1895, at the dawn of psychoanalysis as the theory and therapy, psychoanalysis and psychotherapy in general have been attempting to establish and develop their biological roots. Numerous external and internal limitations and resistances have been limiting and opposing this process for almost a century. The last two decades brought a significant change in this view, especially following the development of contemporary neuroimaging techniques with their dynamic and functional features and growing interest for mental processes on behalf of neuroscience. The aim of this paper was to review scientific articles on recent advances in the field of neurobiology of psychotherapy, especially neurobiological underpinnings of psychotherapeutic relationship, and point to the new perspectives this knowledge brings. Recent advances in neurobiology and psychotherapy research open the way for the integration of psychotherapy and neurobiology. With this regard, science could contribute to closing the mind-brain gap which has been artificially dividing a human being for centuries. An integrated field enables new scientific perspective for both disciplines with multilayered understanding of mind-brain functioning.