The present contribution discusses the clinical use of functional MRI (fMRI) and its role in the most common neurological diseases. FMRI was found a reliable and reproducible examination tool resulting in a wide distribution of fMRI methods in presurgical evaluation of epilepsy in determining the relationship of eloquent areas and the epileptic focus. Preliminary data suggest that fMRI using memory paradigms can predict the postoperative memory decline in epilepsy surgery by determining whether a reorganization of memory functions took place. Speech-activated fMRI became the most used tool in determining hemispheric dominance. Visual and sensory-motor cortex can also be routinely investigated by fMRI which helps in decision on epilepsy surgery. FMRI combined with EEG is a new diagnostic tool in epilepsy and sleep disorders. FMRI can identify the penumbra after stroke and can provide an additional information on metabolic state of the threatened brain tissue. FMRI has a predictive role in post-stroke recovery. In relapsing-remitting MS an adaptive reorganization can be demonstrated by fMRI affecting the visual, motor, and memory systems, despite preserved functional performance. Much more extensive reorganization can be demonstrated in secondary progressive MS. These findings suggest that the different stages of MS are related to different stages of the reorganization and MS becomes progressive when there is no more reserve capacity in the brain for reorganization. FMRI offers the capability of detecting early functional hemodynamic alterations in Alzheimer's disease before morphological changes. FMRI can be a valuable tool to test and monitor treatment efficacy in AD. FMRI can also provide information about the mechanisms of different therapeutic approaches in Parkinson disorder including drug treatment and deep brain stimulation.