GVHD is a common complication in patients after allo-SCT. Early detection is important because early therapy may improve the outcome. We evaluated contrast-enhanced ultrasound (CEUS) in patients with GVHD to assess typical imaging features. CEUS was performed in nine patients with histologically proven GVHD. As a control four healthy volunteers and six patients with Crohn's disease (CD) were examined. We employed a high-resolution multi-frequency transducer (6-9 MHz) with contrast harmonic imaging. After the injection of 2.4 mL SonoVue (Bracco, Milan, Italy) intravenously data were acquired and stored digitally. Regions of interest were manually placed over the surrounding mesenteric fat, bowel wall and bowel lumen. Maximum signal increase of each compartment was calculated. Patients with CD and GVHD showed significant contrast uptake in the bowel wall. In contrast to CD patients and healthy volunteers, patients with GVHD showed transmural penetration of microbubbles into the bowel lumen. We assume that the damaged gut mucosal barrier in GVHD enables the microbubbles to penetrate through the bowel wall into the bowel lumen. The penetration of microbubbles into the bowel lumen may serve as a novel diagnostic feature for GVHD if confirmed in controlled clinical trials.