Chondrodysplasia in the autosomal recessive cartilage matrix deficiency (cmd) mutant is caused by lack of the proteoglycan aggrecan arising from a mutation in the gene. Homozygous cmd/cmd mice are characterized by disorganisation of chondrocytes in the growth plate, disproportionate dwarfism, cleft palate, and perinatal lethality. We have studied the impact of the aggrecan deficiency on the expression of other matrix genes during the differentiation of chondrocytes in the growth plate of cmd/cmd 18.5 day fetuses. Compared with the wild-type, there are significant differences in the growth plates of cmd mutants in the combinations of co-expression of genes encoding the glycoprotein link protein, proteoglycan syndecan 3, collagens alpha 1 (X) [Col10a1], alpha 2(XI) [Col11a2], and the alternative transcripts of alpha 1 (II) [Col2a1 type IIA form], and alpha 1 (IX) [Col9a1 long and short forms]. The discordance of gene expression in cmd chondrocytes may be additional factors contributing to the disrupted cellular architecture of the growth plate resulting from the primary absence of aggrecan.