A malformation is a morphological defect of an organ, or a larger region of the body resulting from an intrinsically abnormal developmental process. In this analysis of 1421 neonatal autopsies performed between 1984 and 1993, 243 (17.1%) cases showed malformations. The data was analysed to find external cues to internal malformations. Twenty three (85%) of the 27 neonates with various facial abnormalities had associated internal malformations in the form of cardiac (n = 11; 40%), renal (n = 7; 25%), or gastrointestinal (n = 3; 11%) abnormalities and diaphragmatic hernia (n = 2). Sixty seven neonates had neural abnormalities. These were associated with cardiac (n = 7; 10%), renal (n = 12; 18%) or gastrointestinal (n = 7; 10%) abnormalities; 43 cases, however, did not have any associated malformations. Renal malformations (n = 66) had highest association with skeletal abnormalities (n = 9; 22%). As many as 45(76%) of the 59 cases with cardiac abnormalities had no external anomalies. Five cases of hypoplastic lungs were seen, all associated with external malformations.