Patients with hypertrophic cardiomyopathy (HCM) may have delayed septal activation and left ventricular (LV) mechanical dyssynchrony, and may improve after alcohol septal ablation (ASA). This study used phase analysis of gated SPECT myocardial perfusion imaging (MPI) to evaluate septal activation and LV dyssynchrony in HCM patients pre- and post-ASA. Phase analysis was applied to 28 controls, and 32 HCM patients having rest MPI pre- and post-ASA to assess septal-lateral mechanical activation delay (SLD) and consequent LV dyssynchrony. In addition, phase analysis was applied to another group of 30 patients having serial MPI to measure variability of the LV dyssynchrony parameters on serial studies. ASA significantly reduced SLD and improved LV synchrony in the HCM patients with SLD<0° due to earlier activation of the lateral wall relative to the septum. Based on the measured variability, 12 HCM patients had significant (Z<-1.65, P<0.05) and 4 had moderate (Z<-1.00, P<0.15) improvement in LV synchrony post-ASA. SLD<0° predicted improvement in LV synchrony after ASA with a sensitivity of 81% and a specificity of 88%. SLD and LV dyssynchrony were frequent in HCM patients. HCM patients, whose septal activation became later than lateral activation, had significant reduction in septal activation delay and improvement in LV synchrony after ASA. © Springer Science+Business Media, B.V. 2011.