BackgroundHeterotaxy syndrome (HS) is characterized by a wide variety of cardiac and extra-cardiac malformations, including pulmonary valve stenosis, interruption of the inferior vena cava, total anomalous pulmonary venous connection (TAPVC), asplenia, polysplenia, intestinal malrotation, and preduodenal portal vein (PDPV). We report the case of a heterotaxic infant with an infracardiac TAPVC and preduodenal portal vein who experienced repetitive hemodynamic instability during urgent laparotomy for duodenal obstruction.Case presentationA 3-day-old boy with HS was planned to undergo urgent laparotomy for duodenal atresia. Echocardiogram showed an interrupted inferior vena cava, single right ventricle, pulmonary valve stenosis, and infracardiac TAPVC. On exploratory laparotomy, intestinal malrotation characterized by Ladd’s band was found. During further exploration, repetitive severe hypotension and hypoxia occurred. Thorough examination revealed a greatly dilated PDPV crossing over and compressing the proximal duodenum externally. Finally, we considered the possibility that surgical manipulation directly compressed the dilated PDPV into which the TAPVC had pulmonary venous drainage, leading to repetitive pulmonary venous obstruction (PVO). Computed tomography, which was examined after laparotomy, indicated that the vertical vein from pulmonary venous confluence drained into the portal vein.ConclusionPDPV is a rare anomaly associated with HS. In case of intestinal malrotation and duodenal obstruction in HS with infracardiac TAPVC, both the presence of PDPV and the possibility of pulmonary venous drainage into the PDPV should be considered by pediatric surgeons and anesthesiologists performing laparotomy to avoid catastrophic PVO.