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Fraser syndrome (OMIM 219000) is a rare, autosomal recessive disorder characterized by cryptophthalmos, cutanaeous syndactyly, malformations of the larynx and genitourinary tract, craniofacial dysmorphism, orofacial clefting, mental retardation and musculoskeletal anomalies. There is marked interfamilial clinical heterogeneity. However, there is strong phenotypic similarity and concordance of the degree of severity of the disease within a family. We report a family with two cases of Fraser syndrome with marked clinical heterogeneity. One case had lethal phenotype with bilateral renal agenesis, while the other had mild phenotype with normal kidneys. It has not been reported before and highlights the importance of careful screening of pregnancies in families with Fraser syndrome.