Background: Fecal calprotectin (FC) has been used as a diagnostic marker in intestinal inflammatory conditions. Objectives: As a few studies have been dedicated to assess the role of FC in coeliac disease (CD), the current study aimed to address this issue. Methods: This study included 70 newly diagnosed CD (Marsh score 3) and 70 healthy children. The study was performed at the pediatric ward of Amir-Al-Momenin Hospital in Zabol city, the southeast of Iran, during June 2016-September 2017. The FC level was determined using a specific ELISA kit. Results: Women constituted 64.3% (45/70) and 55.1% (38/70) of CD and healthy children, respectively (P = 0.1). Three was no significant difference in the mean age between children with CD (6.3 ± 3.4) and without CD (8.3 ± 4.5) (P = 0.2). The mean level of FC was significantly higher in patients (239.1 ± 177.3 µg/g) than in healthy controls (38.5 ± 34.6 µg/g, P < 0.001). The titer of anti-tTG was significantly higher in patients than in healthy children (205.9 ± 156.2 U/mL vs. 6.7 ± 2.1 U/mL, respectively, P < 0.001). There was a significant correlation between the FC level and anti-tTG titer (r = 0.611, P < 0.001). However, the correlation was not statistically significant between FC and age (r = -0.154, 0.07). The ROC curve analysis revealed an AUC value of 0.893 (95% CI: 0.827 -0.960, P < 0.001). At the level of 50 µg/g, FC rendered the sensitivity and specificity of 90% and 92%, respectively, for the diagnosis of CD.Positive predictive value (PPV) and negative predictive value (NPV) of FC at this cutoff value were 95.5% and 90.5%, respectively. Conclusions: FC can be considered a screening complementary tool for detecting CD with high sensitivity and specificity.