Mutations in CDH3 gene, encoding P-cadherin, are responsible for hypotrichosis with juvenile macular dystrophy (HJMD), which is a rare autosomal recessive disorder. The HJMD is characterized by congenital sparse hair on scalp and progressive severe degenerative changes of the retinal macula which leads to variable degrees of blindness. The present study reports a large consanguineous Pakistani family with six individuals affected with HJMD. Genotyping using polymorphic microsatellite markers showed linkage of the family to CDH3 gene on chromosome 16q22.1. Sequence analysis of the CDH3 gene revealed a novel splice site mutation (c.IVS10-1 G → A) in intron 10, which leads to skipping of exon 11 and probably synthesizing a non-functional premature truncated protein.