Provided is a method and apparatus for segmenting medical images. The apparatus sets a first seed group including voxels belonging to a segmentation target region among voxels of a medical image and a second seed group including voxels belonging to a remaining region thereof, assigns a weight to a link between a start node and an end node and a voxel node, and segments the medical image into two regions by cutting a link having a minimum weight in a shortest path in which a sum of weights of a path connecting the start node and the end node is minimum.