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Background The burden of pulmonary disease in children with congenital heart disease (CHD) remains under recognized. Studies have examined children with single ventricle (1V) and two ventricle (2V) heart disease and document a decreased forced vital capacity (FVC). Our study sought to further explore the pulmonary function of children with CHD. Methods A retrospective review was performed of spirometry in CHD patients over a 3 year period. Spirometry data was corrected for size, age, and gender, and analyzed using z-scores. Results The spirometry of 260 patients were analyzed. 31% had 1V (n = 80, 13.6 years (IQR 11.5–16.8)) and 69% had 2V circulation (n = 180, 14.4 years (IQR 12.0-17.3)). 1V patients were found to have a lower median FVC z-score compared to 2V patients (p = 0.0133). The prevalence of an abnormal FVC was 41% in 1V patients and 29% in 2V patients. 2V patients with Tetralogy of Fallot (TOF) and Truncus Arteriosus (TA) had similar low FVC comparable to 1V patients. The number of cardiac surgeries predicted an abnormal FVC in 2V patients except TOF patients. Conclusion Pulmonary morbidity in patients with CHD is common with a decreased FVC noted in 1V and 2V patients. FVC is lower in patients with 1V circulation, however, 2V patients with TOF or TA have similar lung function in comparison to the 1V group. The number of surgical interventions was predictive of FVC z-score in some but not all 2V patients and not predictive in 1V patients suggesting a multifactorial etiology to pulmonary disease in children with CHD.