Objective: Visual examination and severity quantification are essential for clinical decision making in patients with pectus excavatum. Yet, visual assessment is prone to inter- and intra-observer variability and current quantitative methods are inadequate. This study aims to develop and evaluate a novel, automatic and non-invasive method to objectively quantify pectus excavatum morphology based on three-dimensional images. Methods: Key steps of the automatic analysis are normalization of image orientation, slicing, and computation of the morphological features encompassing pectus depth, width, length, volume, position, steepness, flaring, asymmetry and mean cross-sectional area.