Blastocystis is an unusual enteric protozoan parasite of humans and many animals whose pathogenic potential is still controversial. To increase the understanding of the molecular epidemiology of this emerging parasite and due to its potential impact on public health, its subtypes (STs) in Iranian symptomatic and asymptomatic individuals were determined. A total of 100 Blastocystis isolates by microscopy and culture methods were obtained. DNA was extracted from the positive culture isolates, and the Blastocystis subtypes were identified using seven subtype-specific sequenced-tagged site (STS) primers. Four subtypes, ST3 as dominant (53 %), followed by ST1 (48 %), ST5 (33 %), and ST2 (7 %) were identified. In this study, ST1 in gastrointestinal patients compared to asymptomatic individuals was significantly dominant (p = 0.001). From 33 (33 %) mixed subtype infections, ST1, 3 (14 %) was significantly related to GI symptoms (p = 0.045), and eight mixed infections with three different STs, which are under reported, were also identified.
