This study determined Blastocystis spp. infection in patients with different classes of IBS. It also detected the sensitivity and specificity of microscopy, Jones' medium and PCR in detecting Blastocystis spp. in IBS patients' stool samples. This cross sectional study was carried out during the period from December 2014 to November 2016. The 100 IBS patients were 57 males and 43 females. Stool samples were collected from IBS patients and were examined by direct wet mount, different stains, cultured on Jones' medium and PCR to detect Blastocystis spp. Blastocystis spp. infection was common in the age group (15-30) "41.5%" and in rural areas "80.5%".The percentage of Blastocystis spp. positive cases detected by direct smear, Giemsa stain, modified trichrome stain, culture on Jones' medium and PCR were 69%, 77%, 80%, 82% and 54% respectively. Blastocystis spp. infection was more prominent in IBS- C class "56.1%". Blastocystis spp. infection was either single or mixed with other infections. The study showed that Blastocystis spp. infection was common in IBS patients especially IBS-C class. Modified trichrome stain and culture on Jones' medium were recommended to be the best methods
used for its laboratory diagnosis.