Parasites are one of the important causal agents of GI disorders. About one third of people all over the world are infected with intestinal parasites. These infections are still a hygienic problem, particularly in developing countries. In this study, 40 patients with inflammatory bowel disease, 40 patients with irritable bowel syndrome & comparative control group were investigated aiming to study the association of IBD and IBS with some intestinal parasitic infections. Stool analysis by different techniques results that the rates of infection among IBD & IBS cases were higher than the controls. Microsporidia was the highest percentage of infection among IBD cases as compared to IBS cases & controls followed by flagellates & amebae and intestinal coccidia. This was followed by B. hominis, E. histolytica, Precyst-E.histolytica, D. fragilis & G. lamblia. Cryptosporidium was the most coccidian detected then by Cyclospora.Concerning host factors, IBD cases showed higher risk of infection in comparison to controls. On the contrary IBS cases showed lower risk of infection. This is expressed by the higher odds ratio regarding gender and the age groups from 10 years old to less than 50 year