Chronic gastrointestinal illness of unknown etiology is a significant problem in the United States. Using a real-time LightCycler PCR assay we detected Blastocystis in nine patients from a metropolitan area of Corvallis, Oregon who presented with diarrhea, abdominal pain, fatigue, joint pain, skin rash and psychiatric co-morbidity. Phylogenetic analysis identified six infections with Blastocystis sp. subtype 3, and one with subtype 1, using the standard Stensvold nomenclature. Most patients with subtype 3 had previously tested negative with conventional parasitological diagnostics, had been symptomatic for over 4 years, and reported antibiotic failure.