Heterotaxy syndrome is a rare but well-known occurrence involving a complex entity of broad-spectrum anatomical anomalies that are associated with various visceral and vascular variants. Authors report an exceedingly rare case of a heterotaxy syndrome with polysplenia in a 44-year-male who underwent a laparoscopic hiatus hernia repair. Preoperative evaluation by a multi-detector computed tomography showed a right-sided stomach, a two-humped left-sided liver, polysplenia, a pre-pancreatic portal vein and an absent inferior vena cava with a direct continuation of the azygous and hemiazygous veins. During the laparoscopic repair following informed consent; the small intestines were normally positioned, and the pancreas was normal in both location and structure. One splenic mass on the left side was lying in the lesser sac beneath the left lobe of the liver and was obscuring the critical view of the esophageal hiatus and the gastric fundus was not redundant and difficulty identifiable, so a superior hiatal repair with Dor fundoplication was successfully performed as it was a safer option. Despite the rarity of such unusual occurrence, a careful preoperative identification of the anatomical anomalies, anticipation of operative challenges and considering alternative techniques are the key to achieve a safe outcome in the context of the aberrant anatomy.