One of the major secreted proteins of human articular chondrocytes in monolayer or explant culture and of synovial fibroblasts is a glycoprotein with an apparent molecular weight of approximately 39,000, referred to as human cartilage glycoprotein-39 (HC gp-39). The protein was purified, and its complete cDNA sequence was determined. It contained an open reading frame coding for a 383-amino acid long peptide. Comparison of the deduced amino acid sequence with known sequences revealed that HC gp-39 contained regions displaying significant homology with a group of bacterial and fungal chitinases and a similar enzyme found in the nematode, Brugia malayi. In addition significant homologies were observed with three mammalian secretory proteins of as yet unknown function, suggesting that a related protein family exists in mammals. The human protein does not possess any glycosidic activity against chitinase substrates, arguing against any function as an endoglycosidase with specificity for N-acetylglucosamine. Analysis by Northern blotting and by reverse transcription/polymerase chain reaction showed mRNA for HC gp-39 to be present in human articular chondrocytes as well is in liver, while mRNA was undetectable in muscle tissues, lung, pancreas, mononuclear cells, or fibroblasts. Neither the protein nor mRNA for HC gp-39 was detectable in normal newborn or adult human articular cartilage obtained at surgery, while mRNA for HC gp-39 was detectable both in synovial specimens and in cartilage obtained from patients with rheumatoid arthritis. These observations suggest that the expression of HC gp-39 may be related to a response of these cells to an altered tissue environment.