Background. Congenital malformations of the gastrointestinal (GI) tract are common birth defects detected in the neonatal period and usually present with signs of GI obstruction which at times can be life threatening. Anorectal malformations are among the more frequent congenital anomalies. The co-occurrence of congenital heart defect (CHD) along with GI malformation can significantly affect the natural history of either defect. Purpose - to study the prevalence of GI malformations in children with CHD and study the risk factors. Materials and methods. A total 100 patients of GI malformations were enrolled out of which 66 (66%) were males and 34 (34%) were females. All patients with any GI malformations (anorectal malformation, tracheoesophageal fistulae, anterior abdominal wall defects) presenting to Neonatal Intensive Care Unit (NICU), Paediatric Cardiac unit, Pediatric and Pediatric surgery outpatient department (OPD) as well as In-patient department (IPD) between October 2019 to October 2021 were included in study. A detailed history and examination was done followed by echocardiography and the prevalence of CHD among GI malformation was observed and risk factors were studied. Results. Most common GI anomaly was anorectal malformation (71%) followed by tracheoesophageal fistula (17%), CHD was seen in 14 children. Most common heart defect was ventricular septal defect (VSD) (43%) followed by patent ductus arteriosus (PDA) (36%) and atrial septal defect (ASD) (14%). Among cases with anorectal malformation, CHDs was seen in 10% and the most common defect was VSD (43%). Forty one percent of cases with tracheoesophageal fistula had CHDs with PDA (57%) being the most common underlying defect. Functional heart defects were present in 28 children of GI malformations. Conclusions. The coexistence and severity of CHD in patients with GI malformation can have prognostic implications. Thus, early cardiac evaluation should be performed in every case of GI malformation, preferably with echocardiography. This is likely to help in the risk stratification as well as management of such children. The study was performed in accordance with the principles of the Declaration of Helsinki. Study is approved by Ethical Committee of the Institution. Informed consent of patients was obtained for the study. No conflict of interests was declared by the authors.