Atrial fibrillation (AF) may appear during the natural clinical course of hypertrophic cardiomyopathy (HCM).It is regarded as a complication of HCM and is a marker of advanced disease. AF is more likely to occur in untreated, obstructive HCM. Unfortunately, this represents a turning point that puts patients at increased risk of further disability, stroke and death. The presence of obstruction is an indication to proceed with septal myectomy to improve or resolve symptoms by ameliorating diastolic dysfunction. If the patient has concomitant AF, a Maze procedure should be added to the septal myectomy. This combined operation yields excellent hemodynamic benefits and potentially decreases the risk of thromboembolic events.