Background: In this study, we aimed to investigate whether septal myectomy is an effective treatment method in the patients with obstructive hypertrophic cardiomyopathy (HCM) and to evaluate early and mid-term results. Methods: Between January 1997 and August 2008, 40 patients (23 males, 17 females; mean age 37.8 +/- 16.8 years; range 7 to 76 years) who underwent septal myectomy for HCM were retrospectively analyzed. The left ventricular outflow tract (LVOT) gradient and septum thickness were assessed using transthoracic echocardiography before and after surgery. Results: The mean preoperative functional capacity of the patients was 2.4 +/- 0.5, the mean LVOT gradient was 97.7 +/- 27.6 mmHg and the mean interventricular septum thickness was 1.7 +/- 0.3 cm. Postoperative early mortality was 5%. The mean follow-up after septal myectomy was 41.9 +/- 33.0 months (range 2-130 months). During follow-up, the mean functional capacity (1.0 +/- 0.2), the mean LVOT gradient (19.1 +/- 10.2 mmHg) and the mean interventricular septum thickness (1.3 +/- 0.2 cm) were statistically significant, compared to the preoperative values (p<0.05). Conclusion: The LVOT gradient may be relieved almost completely using septal myectomy, which is a safe and effective procedure, with satisfactory surgical mortality and morbidity rates and significant recovery of the functional capacity may be also achieved.