A system and method for vertebrae and intervertebral disc localization in magnetic resonance (MR) images is disclosed. In this method, a target spine MR image is segmented by generating a binary segmentation. A spinal cord line is then estimated on the segmented image. Neighboring vertebrae in a region of interest around the estimated spinal cord line are then localized by labeling vertebral regions based on characteristics, such as size and shape, of regions of connected segmented pixels within the regions of interest. A center point of an intervertebral disc between the neighboring vertebrae is then calculated by finding a point halfway between respective borders of the vertebral regions on a line connecting the centers of mass of the vertebral regions.