Extensive genomic polymorphism was demonstrated among morphologically identical B. hominis isolates. A genetic diversity would be a powerful tool for identification or classification of B. hominis subtypes. In this study, 14 Egyptian B. hominis isolates were collected, 5 of them were isolated from asymptomatic people whose infections were detected during routine medical check-up and 9 were isolated from patients with gastrointestinal symptoms. Restriction fragment length polymorphism (RFLP) analysis of PCR amplified small-subunit rDNA (SSU rDNA) was used to study genetic diversity of B. hominis isolates by 3 different restriction enzymes (Hin-fI, RsaI & Sau3AI). Cluster analysis of the riboprint patterns showed 7 distinct genotypes out of 14 B. hominis isolates, 4 were previously reported riboprints and 3 were new ones. The frequency of intestinal symptoms was 64% in Blastocystis cases. Abdominal pain was the most frequent symptom 78% (7/9). There was no definite correlation between RFLP-banding pattern or genetically distinct genotypes and pathogenecity.