The management of apical ventricular septal defects continues to be challenging because of the difficulty in achieving a complete closure without a left apical ventriculotomy. In this study, we present our innovative technique of closing multiple and/or large muscular apical ventricular septal defects through a right atriotomy. We operated three patients with multiple apical muscular trabecular ventricular septal defects (“Swiss cheese”) using a technique that involved exclusion of the right ventricular apex. Their ages ranged between 2 months and 13 years. The VSDs were approached through right atriotomy. The trans right atrial approach using a 5–0 polypropylene purse-string suture or a two-patch procedure is a novel method of closing large apical ventricular septal defects. It was found to be effective with no persistent residual defects and did not have the disadvantages of a ventriculotomy.