Purpose: Calprotectin is a cytosolic protein with immunomodulatory, antimicrobial, and antiproliferative actions. The concentration of calprotectin increases in infection, inflammation, and malignancy. We determined if calprotectin can be used as a marker for the diagnosis and follow-up of bowel inflammation in cow's milk protein allergy (CMPA). Methods: In total, 32 patients newly diagnosed with CMPA were included (24 IgE-mediated, 8 non-IgE-mediated). In all subjects, a complete blood count, total IgE, cow's milk-specific IgE, and fecal calprotectin (FC) were assessed before and after a cow's milk protein (CMP) elimination diet was started. The results were compared with those of 39 healthy children. Results: The mean FC value before the CMP elimination diet was 516 ±311 μg/g in the 32 patients with CMPA and 296 ±94 μg/g in the control group (P=0.011). The mean FC value after the diet in these patients was 254 ±169 μg/g, which was significantly different from the mean value before the CMP elimination diet (P <0.001). When we compared FC levels before the CMP elimination diet in the IgE-mediated group with the control group, we found no significant statistical difference (P=0.142). The mean FC value before the CMP elimination diet was 886 ±278 μg/g in the non-IgE-mediated group and 296 ±94 μg/g in the control group; this difference was statistically significant (P <0.001). In the IgE-mediated and non-IgE-mediated groups, FC values after CMP elimination diet were 218 ±90 μg/g and 359 ±288 μg/g, respectively, and FC values before CMP elimination diet were 392 ±209 μg/g and 886 ±278 μg/g, respectively; these differences were statistically significant (P=0.001 and P=0.025, respectively). Conclusions: FC levels may be a useful marker for follow-up treatment and recurrence determination in CMPA. © The Korean Academy of Asthma, Allergy and Clinical Immunology.