Magnetic Resonance Elastography (MRE) is an MRI-based technique that is used for the clinical diagnosis and staging of liver fibrosis by quantitatively measuring the stiffness of the liver. Due to the complexity of the signal characteristics and the presence of artifacts both in the acquired images and in the resulting stiffness images, the selection of the ROI for the stiffness measurement is currently performed manually, which may lead to significant inter- and intrareader variability. An algorithm has been developed to fully automate this analysis for liver MRE images. Automated segmentation of liver MRE images is challenging due to signal inhomogeneity, low contrast, and variability in patient anatomy. An initial liver contour is found by fitting Gaussian peaks to the image histogram and selecting the peak that comprises intensities in the expected range and produces a mask near the expected location of the liver. After correction to reduce intensity inhomogeneity, an active contour based on intensity, with morphology used to implicitly enforce smoothness, is used to segment liver tissue while avoiding blood vessels. The resulting mask is used to initialize another segmentation which splits the region of the elastogram belonging to the liver into homogeneous liver tissue and areas with inclusions, partial volume effects, and artifacts. In a set of 88 cases the algorithm had a -6.0 ± 14.2% stiffness difference from an experienced reader, which was superior to the 6.8 ± 22.8% difference between two readers. The segmentation was run on an additional 200 cases and the final ROIs were subjectively rated by a radiologist. The ROIs in 98% of cases received an average rating of "good" or "acceptable.