Intestinal obstruction such as atresia coli causes pathophysiological changes in gastrointestinal tissue due to the rise of intra-abdominal pressure. The aim of this study is to determine the intestinal damage with intestinal biomarkers in calves with atresia coli. The study was conducted on 40 Holstein calves diagnosed with atresia coli with mild to moderate abdominal distention and 10 healthy Holstein calves which served as the control. Blood samples were collected from all calves, and then serum concentrations of intestinal biomarkers were estimated, namely intestinal fatty acid binding protein (IFABP), liver fatty acid binding protein (LFABP), trefoil factor 3 (TFF3), and intestinal alkaline phosphatase (IAP), using commercially available specific bovine ELISA kits. An automatic blood gas analyser was employed for determining the lactate concentration. The concentrations of serum LFABP (P < 0.01), IFABP, TFF3, IAP, and blood lactate (P < 0.001) were significantly higher in calves with atresia coli than in healthy calves. The calves affected with atresia coli exhibited severe intestinal damage, and IFABP, LFABP, and TFF3 have significant diagnostic importance and play a useful role in determining the intestinal damage due to intestinal obstruction. High levels of IAP and lactate may serve as a signal for the development of intestinal injury.