Introduction: Fecal calprotectin is known to be a biomarker of inflammatory bowel problems. An increase in its level has been also noted in COVID-19 patients, which is associated with the pathogenic effect of the virus on the intestinal epithelium involving components of nonspecific immunity. Objective: To evaluate markers of local and systemic inflammation and their relationship in the diarrhea syndrome associated with the novel coronavirus disease (COVID-19). Materials and methods: We have analyzed medical histories of 90 laboratory-verified SARS-CoV-2 patients aged 35 to 70 years and divided them into three equal groups of 30 cases each by the measured level of fecal calprotectin (Group 1: CPT > 200 μg/g, Group 2: CPT = 50 to 200 μg/g, and Group 3: CPT < 50 μg/g). Results: In Group 1 patients with CPT > 200 μg/g, we observed a 1.5 times more frequent severe course of the coronavirus disease, pulmonary damage over 50 % (p < 0.05), fever and diarrhea that persisted up to 14.8 ± 0.5 and 8.7 ± 0.4 days, respectively (p < 0.05). Conclusions: We established a direct relationship between markers of local and systemic inflammation. Clinical manifestations of COVID-19 correlated with the severity of intestinal inflammation. A positive correlation was found between fecal calprotectin levels and diarrhea syndrome duration. The landscape of opportunistic intestinal microbiota also correlated with the severity of the inflammatory process in the intestine.