Type IX collagen is a newly discovered collagen molecule that is associated with Type II-containing collagen fibrils in cartilage, vitreous and embryonic cornea. It consists of three distinct chains: alpha 1(IX), alpha 2(IX) and alpha 3(IX). The alpha 1(IX) chain has been to be synthesized in two different forms, which are generated by alternative transcription and splicing. In this manuscript we describe the isolation and sequencing of a cDNA coding for the entire coding region of the long form of mouse alpha 1(IX) chain. Nucleotide sequence analysis of this cDNA determined for the first time the primary structure of the entire long form of the mouse alpha 1(IX) chain. RT-PCR was used to examine collagen gene expression during limb development from day 10 to 18 in mouse embryos. Collagen I and II mRNA levels gradually increased all through the developmental stages. Collagen X expression increased further after day 16 in limb development, whereas the alpha 1(IX)mRNA level dropped at this time. This could be due to active bone formation relative to cartilage synthesis in the embryonic limb bud around day 16 in mouse development.