Purpose: The cow’s milk-related-symptom-score (CoMiSS) tool was developed as an awareness tool for the assessment of cow’s milk-related symptoms in infants or children.Fecal calprotectin (FC) is a noninvasive biomarker of gut inflammation that can be measured in serum and stool. This study aimed to investigate the relationship between FC levels and CoMiSS scores in infants with cow’s milk protein allergy. Methods: Infants (aged 6–12 months) who were allergic to cow’s milk protein were enrolled prospectively. Following completion of the CoMiSS scoring, the infants were divided into group 1 (positive CoMiSS scores ≥12) and group 2 (negative CoMiSS scores <12). FC was measured using immunoassay. Results: Of the 120 infants enrolled in this study, 60 (50.0%) had positive CoMiSS scores (group 1), while 60 (50.0%) had negative scores (group 2). The mean FC level was higher in the infants in group 1 than those in group 2 (2,934.57 µg/g vs. 955.13 µg/g; p<0.001). In addition, there was a positive correlation between FC and CoMiSS scores (R=0.168, p<0.0001). A FC level of 1,700 µg/g provided a sensitivity of 98.3%, specificity of 93.3%, and accuracy of 95.8% for the diagnosis of cow’s milk protein allergy (CMPA). Conclusion FC measurement may have a role in the assessing infants with CMPA.