With limited time for analysing computed tomography (CT) data in medical emergencies, radiologists and clinicians are not always aware of congenital pathologies, especially in asymptomatic cases. We present a case report of heterotaxy syndrome detected incidentally in a 62-year-old female with massive pulmonary embolism, local saccular aneurysm of the aortic arch and COVID-19. The presented case describes an unusual combination of life-threatening conditions and congenital anomalies. Using the CT angiography, we reported the preserved topography and morphology of the heart chambers. The superior and inferior venae cavae were located on the left, draining into a significantly dilated coronary sinus. Disordered abdominal organ arrangement included midline liver, right-sided stomach, the central location of the short pancreas, malrotation of the intestine, polysplenia, and atypical rise of visceral branches of the abdominal aorta. A comprehensive assessment of CT images promoted verification of undiagnosed congenital anomalies. Prompt recognition of heterotaxy syndrome in life-threatening conditions significantly impacts treatment tactics and should be the course of diagnostic and cautious interventions to reduce further complications. Key words: anatomy, aorta, heterotaxy syndrome, computed tomography angiography, aortic aneurysm, pulmonary embolism, COVID-19.