Osteoarthritis (OA) is one of the most prevalent skeletal diseases. Recently, we identified a novel gene on chromosome 3p24.3, named DVWA (double von Willebrand factor A domains), and its functional variants, which are associated with susceptibility to knee OA. Here we report the cloning and characterization of the DVWA gene. DVWA consisted of seven exons and had four alternative splicing variants, which encoded long (385 amino acid) and short (276 amino acid) proteins (L-DVWA and S-DVWA, respectively). S-DVWA was an N-terminal truncated form of L-DVWA and lacked a signal peptide and a part of a VWA domain. L-DVWA and S-DVWA transcripts were mainly expressed in articular cartilage. Immunoblot analysis using epitope-tagged proteins showed L-DVWA in the conditioned media and S-DVWA only in the cell, consistent with the in silico prediction. We also cloned the murine counterpart of DVWA, which was found to be identical to Col6a4, which has recently been reported. L-DVWA had 73% identity to the N-terminal sequence of the 2,309-amino acid Col6a4 protein. The mouse Dvwa/Col6a4 mRNA was present mainly in the small intestine in embryos and adults, but not in cartilage. The amino acid sequence of L-DVWA was conserved in higher species than chicken, but that of S-DVWA was unique in human. Knockdown of DVWA by siRNAs increased expression of chondrocyte matrix genes. Our study indicates that DVWA is evolutionally very unique, which, together with its specific expression in articular cartilage, suggests its specific role in human cartilage metabolism.