During the differentiation of a mouse chondroprogenitor cell line, ATDC5, an analysis of the transcription cartilage-related genes was carried out using real-time RT-PCR in a semiquantitative fashion. A total number of 104 genes both previously linked to chondrogenesis and hitherto not associated with the development of cartilage were analyzed. Parametric statistics, and unsupervised hierarchical and K-medians clustering approaches were used to analyze the gene expression during the sequential processes of proliferation, condensation, differentiation, maturation, and hypertrophic conversion of ATDC5 cells. The obtained data provided a robust determination of expression patterns that make possible an accurate assessment of the molecular events along the chondrogenic differentiation pathway. In addition, time-course expression profiles were described for eight highly regulated genes that have not been associated with chondrogenesis as yet. These included Cryab, Rcor2, Hig1, Bnip3, Mst4, Calml4, Gng2, and Islr.