There is limited data on the role of intestinal parasites in irritable bowel syndrome (IBS) in South America. We evaluated the association between intestinal parasitism and IBS status in Peru. Intestinal parasites were detected in 43% of the IBS cases and in 51% of the controls (P = 0.4). After excluding those infected by any parasite, the IBS prevalence remained high (22%; P = 0.7). No statistically significant difference was noted between IBS cases and controls in terms of monoparasitism, biparasitism or multiparasitism. Furthermore, the protist Blastocystis sp. was inversely associated with IBS.