The atrial baffle repair (ABR) significantly improved the fate of patients with transposition of the great arteries (TGA). However, these patients show impaired exercise tolerance and some present severe decline of systemic ventricular function. Intrinsic myocardial weakness, low heart rate response to exercise and diastolic filling impairment are discussed to be causative. Forty-nine long-term survivors with TGA (median age 23.7 year) after ABR were catheterized with measured oxygen consumption in four conditions (baseline, volume, atrial pacing, dobutamine) and the results were compared to 10 normal controls. Median cardiac output was significantly lower in the ABR group (2.2 vs. 2.6 l/min/m²; p = 0.015), and systemic resistance was significantly elevated (28.9 vs. 22.2 U m²; p = 0.04) in comparison with normals. While stroke volume rose by 27% in the control group, it dropped by 7% in patients after ABR at atrial pacing (80/min). Stroke volume increase after dobutamine was significantly lower after ABR in comparison with normal controls (34 vs. 106%; p = 0.001). Higher NYHA class (p = 0.043), degree of tricuspid regurgitation (p = 0.009) and ventricular function (p = 0.028) were associated with lower stroke volume increase. Limited exercise capability of patients after ABR for TGA is primarily due to limited diastolic filling of the ventricles due to stiff non-compliant atrial pathways. Elevated systemic resistance may lead to severe myocardial hypertrophy with possible ischemia and contribute to the multifactorial decline of ventricular function in some patients.