Despite a more physiological morphology of atrial anastomosis in the bicaval technique with respect to standard biatrial anastomosis in orthotopic heart transplantation (OHT), the impact on the long-term outcome is still not clear. In this retrospective study, we sought to investigate the morphology and function of the atria through magnetic resonance imaging (MRI) and transthoracic echocardiography (TTE). Moreover, we aimed to analyse the accuracy of TTE with respect to MRI. Cox regression analysis of 216 consecutive patients receiving OHT between August 1987 and January 2010 identified only recipient age at the time of transplant to be an independent predictor of mortality (P = 0.048, odds ratio = 1.04). After a mean follow-up of 96.6 ± 77.7 months, 108 patients were alive, of which 35 were found to be eligible for MRI assessment. In this analysis, left and right atrial volumes were found to be significantly larger in the standard group in comparison with the bicaval group (P = 0.001), and no significant difference between the two techniques was observed in left and right atrio-ventricular output. Moreover, a significantly reduced accuracy was observed (CCC < 0.3) when TTE results were compared with MRI assessment in evaluating atrial dimensions. Although left and right atrial volumes are significantly larger in the standard group in comparison with the bicaval group, we concluded that no significant difference in the atrial output and survival between the two techniques could be demonstrated.