A study was undertaken in Jawaharlal Institute of Postgraduate Medical Education and Research, Pondicherry, South India, to understand the relation between congenital developmental disorders and consanguinity and also reproductive wastage and consanguinity. Four hundred children with existing congenital developmental disorders were studied with regard to their consanguineous parentage and compared with 1,000 randomly selected patients attending the paediatric outpatient department. There was a significantly higher prevalence of consanguinity in the study group (p < 0.001) and greater frequency in rural areas. The common types of consanguineous marriages were between first cousins (50.6%) and uncle and niece (42.4%). Frequency of consanguinity was not significantly related to religion and caste. The mean coefficient of inbreeding was 0.056. Consanguinity had no significant effect on average pregnancy rate and reproductive wastage. The frequency of consanguinity was significantly higher especially with autosomal recessive disorders (p < 0.001), congenital heart diseases (p < 0.001), multiple malformations (p < 0.001), neurological malformations (p < 0.005), chromosomal disorders (p < 0.01), genitourinary disorders (p < 0.02) and mental retardation-developmental disorders (p < 0.02). These observations stress the need for communicating the deleterious effects of inbreeding to the public through regular health education.