Craniofrontonasal syndrome is characterized by coronal craniosynostosis, hypertelorism, telecanthus, a broad grooved nasal tip, dental anomalies, mild syndactyly, and broad thumbs. It involves an X-linked malformation syndrome with a variable phenotype that is caused by mutations in the ephrin-B1 gene. Detailed phenotypic analysis indicates that females are more severely affected than males, a highly unusual characteristic for an X-linked disorder. We review the literature on this genetic paradox, and discuss the pattern of inheritance and genetic counseling.