Articular cartilage is recalcitrant to repair and regeneration. Tissue engineering and regenerative medicine are potential strategies to treat the damage to articular cartilage. A thorough understanding of the gene expression profiles in articular cartilage and growth plate chondrocytes will be an important prerequisite for tissue engineering of cartilage. Regeneration is a recapitulation of embryonic development and morphogenesis. We used laser capture microdissection to capture the surface articular chondrocytes and the resting zone chondrocytes of growth plate from 14-day-old C57BL/6J mice. Total RNA was individually purified, pooled, and amplified by two rounds of in vitro transcription. Labeled cRNA probes were analyzed using the Affymetrix GeneChip Mouse Genome 430 2.0 Array. We identified 107 genes that were highly expressed by the surface articular chondrocytes and 130 genes that were highly expressed by the resting zone chondrocytes of growth plate (> or = fivefold). The expression of major matrix proteins aggrecan and collagen II were similar, while several morphogens and growth factors were differentially expressed by the surface articular chondrocytes and the resting zone chondrocytes of growth plate. The results of this investigation will be of use in the evaluation of tissue engineered cartilage.