The purpose of our study was to examine the potential benefits of integrating functional MRI (fMRI) information into the 3D-based planning process for central nervous system (CNS) malignancies. Between 01.01.2008 and 01.12.2009, ten patients with astrocytoma (both low and high-grade histological type) were enrolled in this study. Before the planning process, conventional CT planning, postoperative MR, and individual functional MRI examinations were conducted. For the functional MRI examination four types of conventional stimuli were applied: acoustic, visual, somatosensory, and numeric. To examine the potential benefits of using fMRI-based information, three different types of theoretical planning were applied and compared: 3D conformal plan without fMRI information, 3D conformal plan with fMRI information, and IMRT plan with fMRI information. DVH analysis and the NTCP model were used for plan comparison. When comparing planning methods, distance-related subgroups were generated and studied. By using the additional fMRI information, a significantly higher sparing effect can be achieved on these ORs (both with conventional 3D-based planning and IMRT). In cases when the OR–PTV distance is less than 1 cm, IMRT seems to be a significantly better choice than conventional 3D-based techniques. IMRT also has an additional sparing effect on the optic tract and brainstem, especially for locations close to the midline. Our results demonstrated that using fMRI information in conventional 3D-based treatment planning has the potential benefit of significant dose reduction for the critical organs, with no compromise in PTV coverage even when using conventional 3D planning. fMRI can be widely used in low-grade cases (long life expectancy, lower acute and late toxicity) and also in cases with high-grade astrocytomas or distant metastases (higher dose to PTV with better sparing of risk organs). In cases when the OR–PTV distance is less than 1 cm, IMRT should be the choice of treatment for a higher sparing effect on functional active areas. Longer imaging and clinical follow up are needed to confirm the real sparing effect on these functional areas.