Foramina parietalia permagna (FPP) is an autosomal dominant condition characterized by cranial defects of the parietal bones. It can be present as an isolated feature, but it is also one of the characteristics of a contiguous gene syndrome associated with deletions on chromosome 11p11-p12. One of the proteins known to be involved in skull development is the MSX2 homeobox protein. Previously, MSX2 has been shown to be mutated in patients suffering from Boston type craniosynostosis. We have now analyzed the MSX2 gene in five families affected with FPP. An intragenic microsatellite marker did not reveal any recombination and a cumulated LOD score of +3.2 at theta = 0 was obtained. Sequence analysis further showed that in four out of five families an MSX2 mutation was responsible for the skull defect. Moreover, it appears that FPP is caused by haplo-insufficiency of the MSX2 gene. This implies that Boston type craniosynostosis and FPP are allelic variants of the same gene, with FPP caused by loss of MSX2 function and craniosynostosis Boston type due to gain of MSX2 function.