Video capsule endoscopy (VCE) has proven to be a pain-free imaging technique of gastrointestinal (GI) tract and provides continuous stream of color imagery. Due to the amount of images captured automatic computer-aided diagnostic (CAD) methods are required to reduce the burden of gastroenterologists. In this work, we propose a fast and efficient method for obtaining segmentations of VCE images automatically without manual supervision. We utilize an efficient active contour without edges model which accounts for topological changes of the mucosal surface when the capsule moves through the GT tract. Comparison with related image segmentation methods indicate we obtain better results in terms of agreement with expert ground-truth boundary markings. © The Author(s) 2015.