An unusual combination of syndactylies, macrocephaly, and severe skeletal dysplasia was observed in a newborn infant. A history of digital anomalies in the father and grandfather lead to the diagnosis of dominantly inherited Greig cephalopolysyndactyly syndrome (GCPS, MIM #175700). Having explained the digital findings and macrocephaly, the skeletal changes were thought to fit best congenital spondyloepiphyseal dysplasia (SEDC MIM #183900), a type II collagen disorder. Molecular analysis confirmed the presence of two dominant mutations in the propositus: a GLI3 mutation (E543X), which was present also in the father and grandfather, and a de novo COL2A1 mutation leading to a G973R substitution. Thus, this boy combined the syndactyly-macrocephaly phenotype of Greig cephalosyndactyly syndrome with a severe form of spondyloepiphyseal dysplasia caused by the structural defect in type II collagen. The diagnostic difficulties posed by the combination of two genetic disorders and the contribution of molecular diagnostics are well illustrated by this case.