Chondrocytes surrounded by extracellular matrix are responsible for the maintenance of the cartilage as a functional entity. It is well accepted that chondrocytes cultivated for tissue engineering dedifferentiate in cell culture. We characterized the expression of different collagens and collagen related proteins in differentiated (primary) and cultured nasal chondrocytes by using microarray gene expression analysis and immunohistochemical staining. The genes for collagen subunits 1α1 (Col1α1) and 1α2 (Col1α2) were activated during a cell culture period of 5 and 20 days whereas Col2α1 could be detected both in differentiated and dedifferentiated chondrocytes. The long-term cell culture revealed a late activation of the Col3α1, Col4α1 and Col11α1 genes as well as biglycan, fibromodulin and lumican. In addition, short-and long-term cell culture resulted in down-regulation of Col9α1, Col9α2, Col9α3, Col10α1, Col18α1, ColQ and chondroadherin. The decorin gene showed up-regulation in short-term cell culture, but down-regulation in long-term culture. Immunohistochemical staining of the different cell populations confirmed the mRNA data for collagen type 1, 2, 3, 4, 9α2, 9α3, 18 and decorin. Because of their up-regulation in cultured chrondrocytes the collagen types 1, 3, 4 and 11 as well as biglycan, fibromodulin and lumican may be markers for dedifferentiation. The collagen types 9, 18 and Q as well as decorin and chondro-adherin revealed down-regulation and, presumably, represent markers for the differentiation of chondrocytes.