The N-terminal amino acid sequence of human aggrecan was determined and it was shown that two sequences were present. The major sequence, AVTVE-, accounted for 60% of the aggrecan and started at alanine residue 17 of the human aggrecan core protein cDNA sequence (K. Doege et al. (1991) J. Biol. Chem. 266, 894-920). The other N-terminal sequence, VETX-, started at valine residue 20. Characterization of aggrecan core protein peptides present in the matrix of adult human articular cartilage showed that at least 11 aggrecan core proteins were present with approximate M(r) between 300,000 and 43,000. All these core proteins were found to have the same N-terminal sequences as that observed in human aggrecan. When articular cartilage was placed in explant culture in medium containing 10(-6) M retinoic acid there was a 3.5-fold increase in the loss of aggrecan into the culture medium compared to tissue maintained in medium alone or medium containing 20% (v/v) newborn calf serum. Analysis of the aggrecan core protein fragments that were released to the culture medium containing 10(-6) M retinoic acid showed the presence of 13 core protein peptides of M(r) between 300,000 and 43,000. The 11 smaller peptides of M(r) 230,000 to 43,000 were shown to have the N-terminal sequence ARGS-. This sequence which starts at residue 393 of the human aggrecan core protein is located within the interglobular region between the G1 and G2 domains and is the site of aggrecan catabolism by the putative protease aggrecanase. The presence of core proteins of varying sizes but with the same N-terminal sequence reflects proteolytic processing from the C-terminal end of the core protein that was also observed in the aggrecan macromolecules extracted from the matrix of human articular cartilage. This proteolytic processing was also evident but to a lesser extent in newly synthesized 35S-labeled aggrecan macromolecules.