The purpose of this study was to define a population of visceral heterotaxy and to investigate the incidence of bacterial sepsis in the current era of universal pediatric pneumococcal immunization. Pediatric echocardiography and radiology databases, along with electronic medical records, were searched for patients followed-up since birth between 1999 and 2009 with either asplenia or polysplenia and cardiac anatomy consistent with heterotaxy syndrome. A total of 29 patients were identified. Seven patients (24%) had a total of 8 sepsis events, and 6 patients (86%) developed sepsis while taking appropriately prescribed antibiotic prophylaxis. Of the patients with sepsis, 5 had polysplenia and 2 had asplenia. Sixty-two percent of sepsis events were nosocomially acquired. No cases of pneumococcal sepsis occurred after the introduction of the conjugated pneumococcal vaccination to the pediatric vaccination schedule. Bacterial sepsis was associated with a 44% mortality rate. An unexpected finding in 3 patients with visceral heterotaxy, asplenia, and an interrupted inferior vena cava (IVC) as the only anomaly on echocardiography was associated intestinal malrotation. Children with visceral heterotaxy remain at significant risk of life-threatening bacterial infection. In addition, the finding of interrupted IVC on echocardiography should prompt screening for intestinal malrotation, even in the absence of additional structural heart disease.