Functional Magnetic Resonance Imaging (fMRI) permits the non-invasive mapping of brain activation during some specific stimulation. This paper demonstrates the application of fMRI for including cortical activation into a treatment plan produced on our commercial treatment planning system (CMS XiO™). A patient with an intracranial tumour near the motor cortex was studied on a 1.5 Tesla GE Signa scanner. Images from conventional MRI, used to define the planning target volume (PTV), and from fMRI, used to define the organ at risk (OAR), were transferred to the treatment planning system. Three plans were generated with similar treatment intent and compared to assess the dose given to the OAR. These were: 1. a conventional plan; 2. an IMRT plan optimised to cover the PTV and; 3. an IMRT plan optimised to additionally spare the OAR. Results show that 21% of the motor cortex (OAR) receives 90% of the prescription dose when planned conventionally. This is reduced to 9% when IMRT is used, and to 2% when fMRI data is included. This novel approach can be extended to other functional areas of the brain, giving rise to a more conformal avoidance radiotherapy technique, which may help to preserve patient's quality of life.