Intestinal acute graft-vs-host disease (GVHD) is a life-threatening complication after allogeneic hematopoietic cell transplantation. Non-invasive diagnostic procedures are still lacking and diagnosis is difficult. We hypothesized that contrast-enhanced ultrasound sonography (CEUS) could detect microcirculation changes of the bowel walls during intestinal GVHD and help to detect and monitor treatment response. We employed CEUS to prospectively evaluate intestinal GVHD in 83 consecutive transplant patients between 2008 and 2011. Fourteen /83 patients with biopsy-proven intestinal GVHD were selected as study group. Fourteen patients with biopsy-proven stomach GVHD without intestinal symptoms (N=16), normal volunteers (N=6) and patients with neutropenic enterocolitis (N=4), were chosen as control group. All patients were evaluated with both standard transabdominal ultrasonography (US) and CEUS at the onset of intestinal symptoms, during clinical follow up and at flare of symptoms. Standard US revealed non-specific bowel wall thickening, and simultaneous involvement of multiple intestinal segments in 9/14 patients. CEUS showed three distinct patterns of microcirculation changes that correlated with GVHD activity. These findings were not observed in the control group. Moreover, CEUS findings correlated with treatment response and predicted flare of intestinal symptoms. CEUS is a non-invasive, easily reproducible bed-side tool to detect and monitor intestinal GVHD.