Cardiovascular disease in the pediatric population closely affects the respiratory system inducing water retention in the lungs and pulmonary edema, airway compression by cardiovascular structures, restrictive pulmonary physiology as a result of hemodynamic changes and surgical repair, susceptibility to respiratory infections, development of pulmonary hypertension, thrombosis, or hemorrhage. Chronic heart failure and congenital heart disease are characterized by various respiratory manifestations and symptoms mimicking lung disease, which are frequently difficult to diagnose and treat. Pulmonary function is multiply affected in pediatric heart disease with mostly restrictive but also obstructive and diffusion abnormalities. Patients with Fontan circulation represent a separate group with slow, passive pulmonary blood flow and distinct pathophysiology with low cardiac output heart failure, restrictive lung pattern, increased thromboembolic complications and rare conditions such as protein losing enteropathy and plastic bronchitis. Distinguishing between cardiovascular and pulmonary symptoms may be challenging in the growing population of pediatric and adult survivors of congenital heart disease and understanding of the relationship of the two systems in heart disease is crucial for the optimal management of these patients.