It is not only the total curative resection of pathological tissue or the minimization of symptoms to be considered in epilepsy surgery or other neurosurgical procedures, it is equally desirable to maintain the best possible quality of life. Cortical mapping methods can help achieve this goal by delineating eloquent areas, i.e. brain regions that are vital for providing an acceptable quality of life, albeit not prone to compensatory reorganization. These areas include among others the Broca and Wernicke regions for speech, the primary motor, sensory and visual cortices. Functional MRI gained importance in the last decade as a non-invasive clinical cortical mapping technique. This method is capable of localizing cortical areas selectively activated by a given task condition. Thus, selecting appropriate tasks can help mapping eloquent brain regions. Using functional MRI provides information that is complementary to other mapping methods. Moreover, it can replace invasive methods such as the Wada test. Here, we explain the background of functional MRI, compare it to other clinical mapping methods, explain the intricacies of paradigm selection, and show the limitations of the technique while also pointing out alternative uses.