Dientamoeba fragilis is a globally occurring parasite that has been recognized as a causative agent of gastrointestinal symptoms. A single-round PCR was developed to detect D. fragilis DNA directly from human stool samples. The genetic diversity of D. fragilis from 93 patients and 6 asymptomatic carriers was examined by PCR followed by restriction fragment length polymorphism and sequencing of part of the small-subunit rRNA gene. The data show that D. fragilis sequences can be studied directly from fecal specimens despite the absence of a cyst stage and without the need for prior culturing. In addition, the results suggest strongly that D. fragilis shows remarkably little variation in its small-subunit rRNA gene.Dientamoeba fragilis is a protozoan parasite found in the mucosal crypts of the large intestines of humans. Originally D. fragilis was considered an ameba, but based on ultrastructural characteristics (2), antibody data (8), and phylogenetic data originating from 16S-like rRNA gene sequences, it has been established that it is a trichomonad (20), with no identified cyst stage. Most recent literature accepts that D. fragilis is an important enteric pathogen (7,10,18), with an estimated incidence of symptomatic infection of between 4 and 91% (11,21,25,26). Symptoms include abdominal pain, bloating, and diarrhea.Because of the lack of a cyst stage, diagnosis can be performed only on freshly passed stool or by the use of fixatives and permanent stains. In addition, day-to-day shedding is highly variable, which imposes the need for multiple sampling (24). These features have likely led to an underestimation of the prevalence of D. fragilis, which is reported to vary between 0.2% and more than 19% depending upon the population studied (3,9,15,16,26).Despite the relatively high prevalence of D. fragilis and its apparent role in patients presenting with gastrointestinal complaints, surprisingly little is known about its pathogenicity, route of transmission, epidemiology, and genetics. Because only some infected persons experience symptoms, it is possible that D. fragilis is a heterogeneous species with nonpathogenic and pathogenic variants with similar morphology but different pathogenicities. This has been suggested for other lumendwelling protozoa such as Giardia duodenalis (13) and demonstrated for Entamoeba histolytica/Entamoeba dispar (4, 6). In a first report on variability in D. fragilis, the 16S-like ribosomal subunit DNA sequence of cultured D. fragilis from a small number of patients was analyzed by restriction fragment length polymorphism (RFLP) (14). Two of the 11 isolates gave a different restriction fragment pattern, indicating that there was genetic diversity in these D. fragilis cultures.The cumbersome and time-consuming techniques to maintain D. fragilis in culture in combination with the rapid disappearance of trophozoites from fresh feces have probably precluded more extensive and detailed studies of the genetic variability in D. fragilis. In addition, culture is not suitable for molecular ana...