A 55-year-old man with a history of cryptogenic stroke presented to the authors' department for investigation. On transthoracic echocardiography, he was found to have a small secundum atrial septal defect, and transesophageal echocardiography was performed for a more detailed assessment. Following this, the defect was deemed suitable for percutaneous closure. The case demonstrates the utility and benefits of live three-dimensional transesophageal echocardiography for the assessment of this type of defect and guidance of transcatheter closure.