Type IX collagen, a member of the FACIT family of collagenous proteins, contains heterotrimeric molecules of distinct alpha 1(IX), alpha 2(IX) and alpha 3(IX) chains. In this paper we describe the assembly and nucleotide sequence of a cDNA encoding the entire mouse alpha 1(IX) collagen chain. The nucleotide sequence provides for the first time the complete primary structure of the mouse chain. Knowledge of the complete structure of mouse alpha 1(IX) collagen will be useful for investigations of type IX collagen expression during normal mouse development and for the generation of transgenic mice with specific defects in this collagen.