A 52-year-old man was referred to the cardiology outpatient service with exertional angina and shortness of breath due to hypertrophic obstructive cardiomyopathy. He underwent transcoronary ethanol septal ablation (TESA) with successful procedural outcome. The patient returned to hospital with a 3-week history of intermittent fever and a positive blood culture showing Staphylococcus aureus, sensitive to flucloxacillin. Transoesophageal echocardiography on admission demonstrated vegetation on interventricular septum and a repeated scan 10 days later demonstrated Doppler flow across the interventricular septum, confirming the presence of a small ventricular septal defect. This patient was successfully managed with 6 weeks of intravenous antibiotics and remained well at 1-year follow-up.