Microvascular dysfunction in hypertrophic obstructive cardiomyopathy (HOCM) depends on a complex interplay of functional and anatomic mechanisms. We used myocardial contrast echocardiography in 16 consecutive patients with HOCM (mean age 49 ± 15 years; 11 men) referred for percutaneous transluminal septal myocardial ablation to assess myocardial perfusion before and 6 months after the procedure. Myocardial contrast echocardiography was performed using real-time imaging during intravenous injection of SonoVue. Myocardial blood velocity (β) and a semiquantitative assessment of blood volume were obtained in the apical 4-chamber views at midapical septum. Twelve healthy individuals served as control subjects. In patients with HOCM, β was lower either before (0.17 ± 0.04 vs 0.50 ± 0.34 s−1, P = .006) or after (0.23 ± 0.07 vs 0.50 ± 0.34 s−1, P = .02) successful percutaneous transluminal septal myocardial ablation compared with control subjects. A patchy perfusion pattern was seen in all the patients with HOCM either before or after the procedure. In patients with HOCM percutaneous transluminal septal myocardial ablation improves, but does not normalize microvascular function.