Ventilation-perfusion (V/Q) scans are commonly performed in patients with suspected pulmonary thromboembolism (PE). V/Q mismatch is typically attributed to PE. We describe a case in which a V/Q scan performed on a patient with advanced hypertrophic obstructive cardiomyopathy showed large areas of V/Q mismatch not due to PE. The mismatch was due to pulmonary hypertension secondary to left-sided heart disease. The pathophysiology is briefly reviewed.