We developed a method to isolate well defined joint specimens from different compartments of normal and arthritic murine knee joints in which mRNA levels of stromelysin and IL-1 were semiquantified using RT-PCR. Joint capsule specimens were isolated on medial and lateral sides of the patella with a biopsy punch. Cartilage layers were isolated from patellae after a mild decalcification with EDTA. EDTA treatment had no effect on the amount and efficiency of amplification of mRNA when tested on isolated chondrocytes. After induction of experimental arthritis, stromelysin mRNA was elevated approximately 50 times in both joint capsule and cartilage. IL-1 was elevated 100 times in joint capsule but only 10 times in cartilage. Kinetic analysis of mRNA levels in cartilage during arthritis showed a prolonged elevation of stromelysin mRNA compared to IL-1. The variation in mRNA levels between joints of individual mice proved to be low, showing that sampling of the specimens and subsequent RT-PCR can be performed reliably. The current method offers a valuable approach to study gene expression in knee joints during murine experimental arthritis.