In this paper, we present an automatic method to segment the kidney in 3D contrast-enhanced ultrasound (CEUS) images. This modality has lately benefited of an increasing interest for diagnosis and intervention planning, as it allows to visualize blood flow in real-time harmlessly for the patient. Our method is composed of two steps: first, the kidney is automatically localized by a novel robust ellipsoid detector; then, segmentation is obtained through the deformation of this ellipsoid with a model-based approach. To cope with low image quality and strong organ variability induced by pathologies, the algorithm allows the user to refine the result by real-time interactions. Our method has been validated on a representative clinical database.