There are inconsistent findings about the role of Blastocystis infection in irritable bowel syndrome (IBS). The present study was aimed to determine the frequency of Blastocystis and their subtypes (ST) in patients with IBS. A total of 122 patients with IBS and 122 healthy individuals referred to the medical laboratory centers in Ahvaz (southwest of Iran) participated in the study. The frequency of Blastocystis was determined. Blastocystis genomic DNA was extracted from positive feces, and PCR was performed using seven primer pairs targeting the SSU rDNA gene. Blastocystis was detected in 19.67% of patients with IBS and 17.2% of individuals without IBS. The difference between two groups was not statistically significant (P = 03). Among the five subtypes of Blastocystis, ST3 was more common in patients with IBS and control group. However, there were no significant differences between two groups in terms of subtypes of Blastocystis (P = 0.6). It seems, the role of Blastocystis in the etiology of IBS should be further investigated. Furthermore, a model of study should be designed to investigate the role of host factors in severity of parasitic disease. (C) 2016 Published by Elsevier Ireland Ltd.