BACKGROUND To evaluate the frequency of Blastocystis hominis parasitation and to ascertain its role as an intestinal a prospective study during 18 months pathogen has been carried out. METHODS The study included 2,039 patients, which were classified in three groups (asymptomatic [group A], with suspicion of parasitosis [group B], with diarrhoea [group C]). In all cases a coproparasitological study was performed. In the group C the presence of non-parasitic enteropathogens was also investigated. In patients with B. hominis in the absence of other pathogens clinical and epidemiological characteristics were evaluated. Also, its was determined the morphology and quantification of parasites. RESULTS Parasites were identified in 26.2% of population. B. hominis was identified in 336 patients (16.5%). The frequency of parasitation was superior in adults (p < 0.0001), with a slight predominance in the female sex. The rate of asymptomatic carriers was 3.3%. In 21 patients B. hominis (group C) was observed in absence of other enteropathogens. Statistical significant association was found between B. hominis, in absence of other pathogens and the presence of clinical manifestations (p < 0.0001), the most common of which were diarrhoea and abdominal pain. We did not find a statistically significant association between the number of B. hominis present and stool characteristics. The vacuolar form was the predominant morphological type. The ameboid form was observed only in diarrhoeal stools. CONCLUSIONS B. hominis is the most frequent parasite found in faecal parasitological investigation. In absence of other causes, B. hominis must be considered as a pathogen.