Only recently has functional neuroimaging been used increasingly in the context of psychotherapy research. Based on a literature survey, procedures, methodological underpinnings and paradigms relevant for psychotherapy research are explored regarding functional magnetic resonance imaging (fMRI) and positron emission tomography (PET). Current studies on changes of brain functions and potential mechanisms are presented based on obsessive-compulsive disorders, depression, phobia, panic and borderline personality disorders. Findings and implications are discussed regarding the use of functional neuroimaging in psychotherapy research. Systematic changes of brain activation were demonstrated following successful psychotherapy, partially resembling and partially differing from those induced by psychopharmacological treatments. Thus the traditional split between pharmacological procedures "acting on the brain" and psychological procedures making the patient "feel better" has been rendered obsolete. Procedures of functional neuroimaging have been developed to such an extent that they can be used to study issues of great relevance for psychotherapy, e. g. biological underpinnings of psychiatric disorders, plasticity of neural networks, mechanisms of change and prognostic factors of psychotherapy, etc. © Springer Medizin Verlag 2006.