The human gut is host to a diversity of microorganisms, including the single-celled microbial eukaryote Blastocystis. Research has shown that most carriers host a single Blastocystis subtype (ST), which is unusual given the considerable within-host species diversity observed for other microbial genera in this ecosystem. However, our limited knowledge of both the incidence and biological significance of Blastocystis diversity within hosts (i.e., so-called mixed infections) is likely due to problems with existing methodologies. Here, we developed and applied Blastocystis ST-specific PCRs for the investigation of the most common subtypes of Blastocystis (ST1 to ST4) to a healthy human cohort (n ؍ 50). We detected mixed infections in 22% of the cases, all of which had been identified as single-ST infections in a previous study using state-of-the-art methods. Our results show that certain STs occur predominantly as either single (ST3 and 4) or mixed (ST1) infections, which may reflect inter alia transient colonization patterns and/or cooperative or competitive interactions between different STs. Comparative analyses with other primers that have been used extensively for ST-specific analysis found them unsuitable for detection of mixed-and, in some cases, single-ST infections. Collectively, our data shed new light on the diversity of Blastocystis within and between human hosts. Moreover, the development of these PCR assays will facilitate future work on the molecular epidemiology and significance of mixed infections in groups of interest, including health and disease cohorts, and also help identify sources of Blastocystis transmission to humans, including identifying potential animal and environmental reservoirs.T he human gut is a complex, open-ended ecosystem that is host to a diversity of microorganisms, including the single-celled microbial eukaryote Blastocystis (1, 2). Blastocystis is a member of the Stramenopiles or Heterokonta branch of the Eukarya (3) and is phylogenetically distinct from other microbial species of Eukarya such as protozoa, molds, and yeasts that also colonize and/or infect the human gut. Blastocystis has a global distribution and is estimated to colonize between 1 billion and 2 billion people worldwide. In addition to humans, Blastocystis spp. are common inhabitants of the gastrointestinal tract (GIT) of a wide range of other mammalian and nonmammalian hosts, such as livestock, primates, reptiles, and insects (4-6). To date, 17 subtypes (STs) have been described, 9 of which have been detected in human populations. The majority of human-associated STs (ϳ90%), however, are categorized into one of four STs (ST1, ST2, ST3, and ST4) (4).One of the most important recent advances in Blastocystis research is the development and application of sensitive PCR methodologies to study the prevalence and diversity of Blastocystis in human populations (7-9). Emerging data from such studies have indicated that there is significant variation in the distribution of Blastocystis STs within and between geograp...