Isomerism, also referred to as “heterotaxy” is a complex set of anatomic and functional perturbations. One of the most obvious manifestations of isomerism is the disturbance of organ arrangement, such that the thoracic organs are no longer asymmetric on the left and right. We report the case of a 14-year-old female in whom exercise-induced dyspnea led to a late diagnosis of left isomerism complicated by Abernethy malformation and portopulmonary hypertension. A comprehensive evaluation revealed two anatomic left lungs and hyparterial bronchi, bilateral left atria, an interrupted inferior caval vein with azygos continuation, multiple spleens, sinus node dysfunction, hepatic hypertrophy with focal nodular hyperplasia, and absence of the portal vein. Pulmonary vasodilator therapy was initiated resulting in clinical improvement. This case exhibits unique features including a late diagnosis of isomerism with Abernethy malformation and portopulmonary hypertension. The patient’s presentation, medical workup, and future treatment emphasise the importance of multidisciplinary care in children with complex multisystem disease. We review the multiple cardiac and extracardiac manifestations of isomerism.