The mechanical function and the collagen phenotype of the disc are complex, each a hybrid of elements of ligament and cartilage. In detail, the collagen properties are unique. Collagens I and II provide the bulk of the tissue fabric interwoven in opposing radial concentration gradients. From analysis of isolated cross-linked peptides, some degree of commingling of these major fibrillar collagens occurs down to the molecular level. Collagens V, VI, IX, XI, XII and XIV all contribute to the matrix. Collagen IX is the short molecular form that lacks a non-collagenous (NC)4 domain, not the long form found in most hyaline cartilages. Protein sequence and reverse transcriptase-PCR analysis confirmed this was the result of expression from the alternative transcription start site, not proteolysis of the long form. In view of recent reports that common single nucleotide polymorphisms in COL9A2 and COL9A3 are linked to chronic sciatica associated with disc pathology, the specific interactions and role of collagen IX in disc tissue are important to define.