Corpus callosum agenesis is a well known feature of certain syndrome complexes of clinical significance namely, Aicardi syndrome, Smith Lemli Opitz syndrome, Klinefelter, Leigh's disease etc. We present a nine month old male child with global developmental delay, chronic constipation, facial dysmorphism, microcephaly, bony deformities and repeated convulsions. Further evaluation revealed presence of ventricular septal defect, genitourinary abnormality, Hirschsprung disease and agenesis of corpus callosum fitting into the diagnosis of Mowat Wilson Syndrome (MWS). By 2007, only 171 cases have been reported worldwide and none from India till date. MWS is primarily a phenotypic diagnosis and genotypically characterized by heterozygous mutation or deletion of zinc finger E box binding homeobox 2 gene, ZEB2 previously called ZFHX1B. Our case had typical phenotypic features of MWS with normal genetic study and certain unreported manifestations. Identification of this unique syndrome complex is important for genetic counseling and rehabilitation based on associated comorbid conditions.