We describe a case of a 50-year-old male with hypertrophic obstructive cardiomyopathy (HOCM) who presented with syncope, progressively limiting dyspnea and chest discomfort. Coronary angiography showed an unusually extreme angle (approximately 130 degrees) to the origin of the major septal artery. After conventional guidewire cannulation failed, use of magnetic navigation with the Stereotaxis Niobe system permitted guidewire and balloon catheter cannulation of the septal artery to facilitate successful transcatheter alcohol septal ablation.