Cystic fibrosis (CF) is a common autosomal recessive disorder with different clinical manifestations, mainly in the gastrointestinal and respiratory tracts. This study was performed to access the effect of probiotics in the status of intestinal inflammation in a group of children with CF by measuring the calprotectin level in the fecal samples. Forty-seven patients with CF were enrolled in this study. The fecal calprotectin levels were measured by enzyme linked immunosorbent assay. In a randomized systematic method, the children were divided into two groups - one group received probiotic powder and another received placebo for four weeks. After this period, fecal calprotectin was re-measured. Thirty-one of 47 enrolled patients (65.9%) had abnormal fecal calprotectin levels (>50 µg/g). After the intervention, the fecal calprotectin levels decreased in 29 patients (21 patients in the drug group, and only 8 patients in the placebo group; p<0.001). This study showed that about two-thirds of patients with CF had intestinal inflammation based on fecal calprotectin levels. Probiotic administration was shown to decrease calprotectin concentrations and subsequently intestinal inflammation in CF patients.