In this paper the authors review the issues associated with bioinformatics and functional magnetic resonance (fMR) imaging in the context of neurosurgery. They discuss the practical aspects of data collection, analysis, interpretation, and the management of large data sets, and they consider the challenges involved in the adoption of fMR imaging into clinical neurosurgical practice. Their goal is to provide neurosurgeons and other clinicians with a better understanding of some of the current issues associated with bioinformatics or neuroinformatics and fMR imaging. Thousands to tens of thousands of images are typically acquired during an fMR imaging session. It is essential to follow an activation task paradigm exactly to obtain an accurate representation of cortical activation. These images are then interactively postprocessed offline to produce an activation map, or in some cases a series of maps. The maps may then be viewed and interpreted in consultation with a neurosurgeon and/or other clinicians. After this consultation, long-term archiving of the processed fMR activation maps along with the standard structural MR images is a complex but necessary final step in this process. The fMR modality represents a valuable tool in the neurosurgical planning process that is still in the developmental stages for routine clinical use, but holds exceptional promise for patient care.