Aggrecan is one of the first proteins to be depleted from articular cartilage in early osteoarthritis. We investigated the molecular differences between matrix metalloproteinase (MMP)- and aggrecanase-mediated aggrecan degradation, as a consequence of their distinct time-dependent degradation profiles. Cartilage degradation was induced by cytokine stimulation in bovine articular cartilage explants and quantified by a dye-binding assay and immunoassays. The size of degradation fragments was analysed by Western blot. Cytokine stimulation resulted in the early release of aggrecanase-mediated aggrecan degradation fragments. In contrast, MMP-mediated aggrecan degradation began only at day 16 and continued to day 21. Western blot analysis showed that glycosylated high-molecular-weight (374)ARGSVI fragments appeared at day 7, in contrast to deglycosylated low-molecular-weight (342)FFGVG fragments which were detected at day 21. Aggrecan degradation may be divided into two different pools, a high-molecular-weight aggrecanase-mediated pool, and a low-molecular-weight MMP-mediated pool. This may have implications for the development of intervention strategies for OA.