Isomerism, also known as heterotaxy, is a clinical entity that impacts multiple organ systems both anatomically and functionally. The airways and lungs are involved in a great number of these patients, leading to increased sinopulmonary symptoms, increased need for oxygenation, and increased postoperative ventilatory support. Additionally, these patients often have congenital heart disease requiring Fontan palliation. What has not been previously described, and is the focus of this study, is the results of cardiopulmonary exercise testing in those who have undergone Fontan palliation with and without isomerism. We have now compared these finding with those from patients with primary ciliary dyskinesia, as many patients with isomerism have ciliary dyskinesia. We identified patients having the Fontan circulation with and without isomerism who had undergone cardiopulmonary exercise testing, comparing the findings from healthy individuals undergoing exercise, and a comparable number of individuals with primary ciliary dyskinesia but no congenital heart disease. We were able to include a total of 68 patients in our study, with 17 in each of the four groups. Cardiopulmonary exercise testing yielded the best results in healthy patients. All patients with the Fontan circulation demonstrated mixed pulmonary disease, although those with isomerism had greater FVC and FEV1. Exercise times did not differ, although peak consumption of oxygen was greater in those with isomerism. Those with ciliary dyskinesia had only obstructive pulmonary disease and had the lowest FEF25-75 between all groups. Those with isomerism had a lesser degree of obstructive pulmonary disease when compared to those with primary ciliary dyskinesia. Patients with the Fontan circulation with and without isomerism have relatively subtle differences in their cardiopulmonary exercise testing, with both groups demonstrating restrictive lung disease. In regard to obstructive lung disease, those with isomerism tend to be more similar to the patients with primary ciliary dyskinesia than those with the Fontan circulation but without isomerism. The results are likely limited by selection bias and highlight the need for multicentric efforts to characterize cardiopulmonary exercise testing in those patients with pulmonary isomerism.