The aims of this study were to assess the development of heart failure in patients with congenitally corrected transposition of the great arteries in a medium-term follow-up, to identify the impact of tricuspid regurgitation on the development of heart failure, and to determine the most reliable marker for its identification. The prospective 6-year follow-up study included 19 adult patients. All patients were evaluated clinically by the determination of N-terminal pro-hormone brain natriuretic peptide levels, exercise stress testing, echocardiography magnetic resonance, or CT. Among them, two patients died of heart failure. There was a decline in exercise capacity and systolic systemic ventricular function (p=0.011). Systemic ventricular ejection fraction decreased (48.3±13.7 versus 42.7±12.7%, p=0.001). Tissue Doppler imaging showed a decline in peak tricuspid systolic annular velocity (10.3±2.0 versus 8.3±2.5 cm/second, p=0.032) and peak tricuspid early diastolic annular velocity (14.6±4.3 versus 12.0±4.5 cm/second, p=0.048). The tricuspid regurgitation did not increase significantly. N-terminal pro-hormone brain natriuretic peptide levels increased (127.0 ng/L(82.3–305.8) versus 226.0 ng/L(112.5–753.0), p=0.022). Progressive exercise intolerance in congenitally corrected transposition of the great arteries appears to be driven mainly by a progression in systemic right ventricular dysfunction. Tricuspid regurgitation is likely to play a role, especially in patients with structural abnormalities of the tricuspid valve – Ebstein anomaly. The N-terminal pro-hormone brain natriuretic peptide levels and tissue Doppler parameters appear sensitive in detecting changes over time and may guide management.