An automatic cortical gray matter segmentation from a three-dimensional brain images is a well-known problem in medical image processing. Determining the location of the cortical surface of the human brain is often a first step in brain visualization and analysis. Due to the complicated and convoluted nature of the cortex, the manual slice by slice segmentation is generally a difficult, inefficient and inaccurate process, which makes an automatic 3D cortex segmentation an important task. In this chapter, we review techniques for automatic 3D MR images segmentation including boundary- and region-based methods, statistical methods, fuzzy clustering and deformable models.