Alcohol septal ablation (ASA) is successful in most but not in all patients with obstructive hypertrophic cardiomyopathy (HCM). We therefore sought to investigate the relation between infarct location versus infarct size with outcome after ASA in patients with obstructive HCM. Baseline characteristics, procedural characteristics, and cardiovascular magnetic resonance findings at baseline and 4–6 month follow-up after ASA were analysed in 47 patients with obstructive HCM in a single-center retrospective study. Infarct size was determined using late gadolinium enhancement. Infarct location was divided into “basal infarction” and “distal infarction” based on an optimal cut-of value of the distance from the basal septum to the beginning of the infarction. A “successful” outcome was defined as 80 % reduction of the invasive gradient with a post-procedural gradient of <10 mmHg. Basal infarctions (n = 31) compared to distal infarctions (n = 16) were associated with successful outcome (100 vs. 38 %, P < 0.001). Larger infarct size (n = 20) compared to smaller infarct size (n = 27) was not associated with successful outcome (75 vs. 82 %, P = 0.72). A more distal location of the infarction, was the only predictor of a less successful outcome (odds ratio 0.76, 95 % confidence interval 0.54–0.98, P = 0.03). Basal versus distal infarctions were also associated with a lower provoked gradient at late (2.6 ± 2.2 years) follow-up (11 (6–20) vs. 27 (12–94) mmHg, P = 0.01). Basal infarctions were associated with a successful outcome after ASA. A larger infarct size was not associated with a better outcome.