Recently developed fMRI can map small functional structures noninvasively and repeatedly without any depth limitation. However, there has been a persistent concern as to whether the high-resolution fMRI signals actually mark the sites of increased neural activity. To examine this outstanding issue, the authors used iso-orientation columns of isoflurane-anesthetized cats as a biological model and confirmed the neural correlation of fMRI iso-orientation maps by comparing them with intrinsic optical imaging maps. The results suggest that highest fMRI signals indeed indicate the sites of increased neuronal activity. Now fMRI can be used to determine plastic and/or developmental change of functional columnar structure possibly on a layer-to-layer basis. In this review, the authors focus mainly on what technical aspects should be considered when mapping functional cortical columns, including imaging techniques and experimental design.