Blastocystis homonis is a common human parasite of uncertain role in human disease. Approximately equal numbers of reports implicate it and exonerate it as a pathogen. Genetic diversity in B. hominis was investigated using riboprinting to study sequence variation in the small subunit ribosomal RNA genes of 30 randomly selected isolates. Extensive sequence variation was discovered in B. hominis ribosomal RNA genes and this species consists of at least seven morphologically identical but genetically quite distinct organisms. If only a subset of the B. hominis variants have the potential to cause disease in humans this might explain the disparate findings reported. Future clinical studies must take the heterogeneity of B. hominis into account.