Heart transplant recipients present a challenge to cardiac multi-detector computed tomography (MDCT) imaging due to high resting heart rates and body mass indices. Previous studies demonstrated the feasibility of coronary allograft vasculopathy detection by MDCT in heart transplant recipients. However, its performance in assessing cardiac structure and function in these patients has not been evaluated. The aim of this study was to compare 64-slice MDCT analysis of cardiac structure and function to 2-dimensional echocardiography in heart transplant recipients. Two independent observers used both semi-automated and automated software to measure chamber dimensions and left ventricular ejection fraction and mass in 20 heart transplant recipients by 64-slice MDCT. Inter-observer variability was determined. The results were compared with echocardiographic measurements provided by another blinded observer. There was moderate agreement between MDCT and echocardiography for chamber dimension measurements, except for left atrial diameter. Ejection fraction by MDCT was slightly lower (mean difference: -2 +/- 9%, p = 0.29) than that obtained by echocardiography and the correlation was moderate (R = 0.49 to 0.54). Left ventricular mass measurements were significantly lower by MDCT (mean difference: -87 +/- 44 g, p < 0.001). Inter-observer agreement for MDCT analysis of left ventricular function (R = 0.90) and mass (R = 0.83) were excellent. These findings demonstrate moderate agreement between 64-slice MDCT and echocardiography in the assessment of chamber dimensions as well as left ventricular mass and function in heart transplant recipients with low inter-observer variability. Also, the addition of cardiac structural and functional analysis to MDCT coronary angiography requires no additional scan time, contrast administration or radiation exposure.