Introduction <p>Heterotaxy syndrome (HS), also termed atrial isomerism or situs ambiguus, is a rare congenital disorder characterized by abnormal left–right arrangement of thoracoabdominal organs. Paraganglioma, a rare neuroendocrine tumor indistinguishable histologically from pheochromocytoma, is classified according to anatomical location and secretory activity. Malignant paragangliomas with metastatic spread are particularly uncommon. To our knowledge, the coexistence of HS and metastatic paraganglioma has not been previously reported.</p> Case Presentation <p> We report a 41-year-old man with a known history of metastatic paraganglioma and secondary polycythemia who presented with sudden right flank and back pain radiating to the groin, along with exertional dyspnea, palpitations, and nocturnal leg cramps. Cross-sectional imaging demonstrated features of situs ambiguus with polysplenia, including mirror-image bronchopulmonary and gastrointestinal structures, multiple spleens located on the right, a transverse liver, and intestinal malrotation. These findings established a previously unrecognized diagnosis of HS. The coexisting metastatic paraganglioma complicated the patient’s clinical course, necessitating careful multidisciplinary evaluation and tailored management.</p> Conclusions <p> This case highlights the diagnostic and therapeutic challenges of managing metastatic paraganglioma in patients with HS. The abnormal anatomical arrangement of organs complicates radiological interpretation, surgical planning, and perioperative care. Recognizing such rare coexistence is critical for accurate diagnosis and risk stratification. To our knowledge, this represents the first documented case of HS with metastatic paraganglioma, underscoring the importance of individualized management strategies in rare disease overlap.</p>