In obstructive hypertrophic cardiomyopathy (HC), extreme heterogeneity of septal morphology makes septal myectomy particularly challenging. Although cardiovascular magnetic resonance (CMR) reconstructs ventricular anatomy with high spatial resolution, CMR is not used systematically to plan preoperatively septal myectomy. In this study, we report our results with using CMR to plan the extent of septal excision in 112 consecutive HC patients who subsequently underwent myectomy. Depth and length of the myectomy planned at CMR were compared with those of the septal muscle excised in a single piece in all patients. Anterior septum maximal thickness at CMR was 22 ± 5 mm and excised muscle thickness 9 ± 3 mm. Planned myectomy length was 35 ± 11 mm (range 17 to 65) and excised muscle length 38 ± 10 mm (range 10 to 70), indicating extension of septal resection to mid-cavity. Thickness and length of the planned myectomy showed a significant correlation with the excised muscle (R2 = 0.345; p <0.001; and R2 = 0.358; p <0.001, respectively). Deep septal crypts were identified at CMR in 12(11%) patients, preventing muscle excision from areas at increased risk of iatrogenic septal defect. Large aberrant muscle bundles that could decrease mid-cavity dimension were identified at CMR and excised in 26(23%) patients. In the 55 patients with postoperative CMR, qualitative comparison of pre and postoperative ventricular morphology showed a smooth and apically extended myectomy. In conclusion, CMR planning of septal myectomy provided high resolution images of septal morphology and allowed us to perform a standardized and apically extended septal excision that was associated with favorable outcome. Our novel approach could make myectomy more accessible to cardiovascular surgeons.