Achondroplasia is the most common human skeletal dysplasia. It is inherited as an autosomal dominant trait but the underlying biochemical cause is unknown. Genomic DNA from 49 affected individuals and two multiplex families with achondroplasia was studied using probes spanning COL2A1, the structural gene for type II collagen. Two lines of evidence speak against mutation in COL2A1 as the cause of achondroplasia: (1) no gross rearrangements are seen on Southern blot analysis of DNA from probands, and (2) linkage studies in multiplex families demonstrate discordant inheritance of achondroplasia and COL2A1 alleles.