Splenic anomalies frequently accompany conotruncal and atrioventricular septal malformations. Asplenia is a major factor in the mortality of newborns with the heterotaxy syndrome, requiring an early and accurate diagnosis. We evaluated the splenic status of five consecutive patients with heterotaxy syndrome by radionuclide splenic scanning with 99mTc-labelled and denatured red blood cells (RBCs) and by real-time abdominal ultrasonography. Examination and comparison of the findings using these diagnostic methods suggest that the former has some diagnostic pitfalls which arise from the symmetrical location of the liver in the abdomen. This leads to difficulty in the interpretation of overlapping signals from the blood pool of the liver and from the spleen.