Background: Myocardial contrast two-dimensional echocardiography (MC-2DE) is widely used to address alcohol septal ablation (ASA) in obstructive hypertrophic cardiomyopathy (HCM). Owing to its limited cut-planes, MC-2DE may inaccurately identify the contrast misplacement associated with an unsuccessful or complicated ASA outcome. Objective: The aim of this study was to assess the added value of myocardial contrast three-dimensional echocardiography (MC-3DE) compared with MC-2DE to identify the appropriate matching between the target septal zone (TSZ) and coronary artery branch for safe and long-term effective ASA in HCM patients. Methods: A consecutive series of 52 symptomatic obstructive HCM patients referred for isolated surgical myectomy (SM) was analyzed with MC-2DE and MC-3DE following injection of echocontrast into one or more septal branches. MC-2DE and MC-3DE patterns were categorized according to complete (Type 1) or incomplete (Type 2) TSZ covering, high-risk (Type 3) exceeding TSZ, or life-threatening outside TSZ distribution (Type 4). Results: MC-2DE per patient analysis showed a Type 1 pattern in 32 patients and Types 2–4 in the remaining 20 patients; subsequent MC-3DE analysis provided a re-phenotyping of MC-2DE findings in 22 of the 52 patients (42%), showing a high-risk Type 2 pattern in 17 of the 32 patients with Type 1, and a new life-threatening Type 4 in three patients with Type 2, respectively. All patients with MC-3DE Type 1 pattern underwent safe and effective ASA with a long-term uneventful follow-up, while the remaining patients underwent SM. Conclusions: Refining high risk or life-threatening contrast misplacement, MC-3DE is more accurate than conventional MC-2DE to target safe and long-term effective septal reduction with ASA in obstructive HCM patients referred for isolated SM.