The objective of this study was to evaluate the role of Blastocystis sp. in gastrointestinal symptoms reported by adult patients in a Peruvian hospital. A case-control 3:1 study was performed at the outpatient clinic. Direct stool examinations were done. One hundred sixty patients were included, 40 cases and 120 controls. Positivity to Blastocystis sp. was associated with dyspepsia (P <0.001), bloating (P <0.001) and abdominal pain (P = 0.03) in patients attending our hospital outpatient clinic.