To determine the distribution of Blastocystis sp. subtypes from Blastocystis cyst excreters, 1,000 fecal samples from patients suspected of enteroparasitic disease were scored for stool consistency, submitted to xenic in vitro culture (XIVC), formol ethyl acetate concentration (FECT) with subsequent isopycnic centrifugation, and polymerase chain reaction (PCR) with subtype (ST) analysis. Blastocystis was significantly more prevalent in specimens from patients with travel-associated diarrhea (15.6%) than those with persistent diarrhea (8.3%) (P = 0.005). Overall, 115 (11.5%) and 35 (3.5%) specimens were positive by XIVC and FECT, respectively. Blastocystis cysts were detected in 33 (28.7%) of the XIVC-positive specimens. A positive FECT result was associated with ST3 (P = 0.05). The presence of Blastocystis in general or Blastocystis cysts was independent of stool consistency, and no particular ST was significantly associated with cyst identification. In view of these data, the present study indicates that Blastocystis cyst formation is independent of Blastocystis sp. subtype and gastrointestinal transit time.