This study evaluated resting pulmonary function and its impact on exercise capacity after atrial baffle (BAFFLE) and arterial switch (SWITCH) repair of D-transposition of the great vessels (DTGV). Previously decreased exercise capacity in DTGV patients has been primarily attributed to cardiovascular limitations, whereas pulmonary limitations have largely been overlooked. Resting flow volume loops were compared for BAFFLE (n = 34) and SWITCH (n = 32) patients. Peak exercise variables were compared for BAFFLE (n = 30) and SWITCH (n = 25). Lung disease (restrictive and/or obstructive) was present in 53% of DTGV patients (BAFFLE 62% and SWITCH 44%; p = 0.14). BAFFLE patients had a normal breathing reserve, whereas that of SWITCH patients was decreased (27.3 ± 28.3 vs. 13.0 ± 19.2; p = 0.04). BAFFLE patients attained a lower percent of predicted peak oxygen pulse (82.7 ± 20.5% vs. 94.7 ± 19.3%; p = 0.04) and peak oxygen consumption (VO(2peak)) (26.6 ± 6.7 ml/kg/min vs. 37.3 ± 8.5 ml/kg/min; p < 0.01) than SWITCH patients. Patients after surgical repair for DTGV have an underappreciated occurrence of lung disease, even post-SWITCH. SWITCH patients have diminished breathing reserves, suggesting a pulmonary limitation to VO(2peak). BAFFLE patients have lower VO(2peaks), greater breathing reserves, and lower oxygen pulses than SWITCH patients, suggesting a cardiac limitation to peak aerobic capacity with probable secondary pulmonary limitations. Treating underlying lung disease in symptomatic patients after repair of DTGV may improve functional status.