Intestinal parasites have a great influence on patients with gastro-intestinal disorders especially those with inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS). This study detected the difference in prevalence of intestinal protozoa among these two groups of patients and evaluated the injury degrees caused by protozoa in gastrointestinal tract (GIT) by measuring the fecal calprotectin (FC) level. This study was done on 219 patients; 101 were IBD patients and 118 were IBS cases attended to the gastroenterology clinics, Zagazig University Hospitals in the period from May 2017 till May 2018 with gastrointestinal symptoms. Stool samples were taken. Microscopic examination for direct wet preparation using 0.9 % of NaCl and 1% of Lugols iodine for each stool specimen was done then confirmed by formol ether sedimentation technique. Fecal smears from sediments of the concentrated samples were stained with modified Ziehl-Neelsen and Trichrome stains. Special ELISA kit was used for calprotectin (FC) fecal detection. Blood sample was taken from each case in EDTA tube for detection of total white blood count, neutrophil percentage, and the hemoglobin content. Out of 219 stool samples, 84 were positive for intestinal protozoa (38.4%); 58(57.4%) of them were patients with IBD & 26 (22%) were patients with IBS. Entamoeba histolytica/dispar, Giardia lamblia, Blastocystis hominis, Cryptosporidium parvum and Cyclospora cayetanensis are the protozoa which were found among the positive cases. Prevalence among IBD was 27(27%), 14(14%), 10(10%), 6(6%) and 1(1%) respectively while among IBS were 10 (8%), 6(5%), 7(6%), 2( 2%) and 1(1%) respectively. High rates of E. histolytica/dispar (27%), G. lamblia (14%), and B. hominis (10%) were among IBD patients as compared with IBS patients (8%, 5%, 6%), P<0.05. Mean fecal calprotectin levels ≥50ng / ml was considered positive and detected in 15 cases (40.5 %) for E. histolytica, followed by 4(20 %) for G. lamblia, 3(17.6 %) for B. hominis and 1(14%) for C. parvum; meanwhile FC level was negative for C. cayetanensis. There was significant correlation P<0.05 among FC, protozoan infections, total WBCs count and neutrophil%.