Objective To review the recent development of functional MRI application in epilepsy. Data sources Both Chinese and English language literatures were researched using MEDLINE/CD ROM (1996-2005) and the Chinese Biomedical Literature Disk (1996-2005). Study selection Published articles about functional MRI application and epilepsy were selected. Data extraction Data were mainly extracted from 38 articles which are listed in the reference section of this review. Results fMRI can be used to localize seizure foci through detecting these cerebral hemodynamic changes produced by epileptiform discharges. EEG-triggered fMRI, which has higher spatial and temporal resolution, helps to detect the spatiotemporal pattern of spike origin and propagation, and define localization of the epileptogenic focus. fMRI is also useful in language and memory cognitive function assessment and presurgical assessment of refractory epilepsy. Atypically distributed cognitive function areas can be detected by fMRI, because of cortical language and memory areas reorganization during long-term epileptic activity in patients with epilepsy. Conclusions fMRI technique plays a very important role in cognitive function and presurgical assessment of patients with epilepsy. It is meaningful for understanding pathogenesis of epilepsy.