The aim of the study was to identify and correlate the anatomical variants of cardiac structures among patients with heterotaxy. In this retrospective cross-sectional analysis of 13 years duration, 302 patients of congenital heart diseases associated with heterotaxy were studied. All these patients had undergone a meticulous clinical evaluation, echocardiography, and cardiac computed tomography. The mean age of the cohort was 38.4 months, with 180 males and 122 females. The cohort had 184 patients of right isomerism and 118 of left isomerism. More than half of the cohort had abnormal pulmonary veins. Over 75% of the cohort had low pulmonary blood flow. Abnormal relationship of great arteries was seen in nearly 69% of the cohort. Atrio-venticular canal defect was the commonest anatomical variant. Overall, 43% of the cohort had single ventricle physiology, predominantly associated with right isomerism. Heterotaxy forms a difficult anatomical subset to comprehend due to the plethora of possible abnormalities. However, unless the cardiac and visceral anatomy is delineated well, the surgical plan becomes suboptimal and often elusive, leaving tough choices for cardiac surgeon. It is essential to obtain all the possible anatomical information using additional imaging modalities to devise a basis for a comprehensive plan for medical and surgical management. A better understanding of the genetic and molecular factors in the etiology, coupled with the application of state-of-the-art imaging techniques, is likely to add to our knowledge of heterotaxy to bring about improved surgical outcomes and a better quality of life for patients suffering from this complex entity.