This study aimed at assessing the possible diagnostic value of cartilage biopsies as a convenient marker for cartilage matrix degradation. We therefore examined cartilage specimens from 56 patients with primary osteoarthritis (OA) of the knee. Resection and biopsy cartilage specimens obtained during joint replacement surgery were used for this study. In addition to histomorphology, immunohistochemistry (ICH) was performed to determine the expression levels and distribution patterns of stromelysin and u-PA protein. The latter data were compared with the degree of histomorphological changes in osteoarthritic cartilage samples, based on a modified version of Mankin's grading score. Compared to the cartilage resection specimens, the biopsies showed comparable expression patterns for both proteinases: the strongest signals were noted in the superficial zone and, as matrix destruction increased, also in the chondrocytes of the transition and deep zones. The strongest signals were ascertained in cell clusters beneath deep matrix fissures. At the immunohistochemical level, we found a direct correlation in the expression of MMP-3 and u-PA between resection specimens and biopsies. Furthermore, in both types of cartilage samples, we noticed a positive relationship between the expression of both proteins and the Mankin score. Analysis of the expression levels revealed significant differences between deep, transition and superficial zones. Histomorphological and immunohistochemical examinations of MMP-3 and u-PA in biopsies of osteoarthritic cartilage turned out to be useful for estimating the pathological changes within osteoarthritic knee joints. Therefore, in future, cartilage biopsies from osteoarthritic knee joints might serve as a diagnostic tool and thus have an influence on further therapeutic strategies.