Type IX collagen is a disulfide-bonded protein first isolated from hyaline cartilage. The structure of this collagen is unusual in that the molecules contain three triple-helical domains interspersed with noncollagenous regions. The molecules are heterotrimers composed of three genetically distinct polypeptide chains. In our laboratory, cDNAs specific for two of these polypeptide chains have recently been isolated. Here we report on the isolation of genomic clones by use of these cDNAs as probes for screening a chicken genomic library. Nucleotide sequence analysis of these clones shows that the exon structure of type IX collagen genes is fundamentally different from the exon structure of the genes for the fibrillar collagen types I-III. Whereas the sizes of exons in fibrillar collagen genes are related to a basic 54-base-pair coding unit, the exons of type IX collagen genes show a large variation in size and do not appear to be related to a 54-base-pair unit. We propose, therefore, that type IX collagen genes belong to a class of vertebrate collagen genes distinct from that of fibrillar collagens.