Transplant-associated thrombotic microangiopathy (TA-TMA) is a severe complication of allogeneic hematopoietic cell transplantation (allo-HCT) with multisystem involvement. Cases of TMA in the intestinal vasculature (intestinal TMA/iTMA) have been reported. We hypothesized that iTMA is a distinct entity from TA-TMA. To test this hypothesis, we prospectively recruited allo-HCT recipients with an indication for endoscopy. Among 20 patients, histological features of iTMA, including loss of glands, total denudation of mucosa, apoptosis and detachment of endothelial cells, mucosal hemorrhage, intraluminal fibrin and microthrombi were found in six. Only 2/6 were classified as GVHD/TA-TMA, while the other 4 as GVHD/no TA-TMA. Gastro-intestinal symptoms were similar between the patients with or without iTMA. With a median follow-up of 11.1 (2.1-67.5) months, 1-year overall survival was 22.2% for iTMA, 55% for GVHD and 60% for TA-TMA. On multivariate analysis, independent unfavorable predictors of OS were iTMA (p = 0.048), HLA mismatched donors (p = 0.008) and gastro-intestinal bleeding (p = 0.021). In conclusion, iTMA emerges as a novel distinct entity in patients with GVHD and/or TA-TMA. Distinct histological features may be useful in differential diagnosis of these severe HCT complications. The higher mortality rates of iTMA than TA-TMA highlight the need for further investigation of this condition.