Although much has been learned about growth plate development and chondrocyte gene expression during cellular maturation and matrix remodeling in the mouse, there has been a limited study of the interrelationships of gene expression between proteinases, growth factors, and other regulatory molecules in the mouse and in other species. Here we use RT-PCR of sequential transverse sections to examine the expression profiles of genes involved in chondrocyte growth, differentiation, matrix assembly, remodeling, and mineralization in the bovine proximal tibial growth plate. Specifically, we studied the expression of genes encoding COL2A1 and COL10A1, the latter a marker of cellular hypertrophy, the matrix metalloproteinases (MMP), MMP-13 and MMP-9, as well as the transcriptional factors, Sox9 and Cbfa1, the growth factors basic fibroblast growth factor (bFGF), parathyroid hormone-related peptide (PTHrP), transforming growth factor (TGF)beta1, and beta2, Indian hedgehog (Ihh), and the matrix protein osteocalcin. These were analyzed in relationship to cell division defined by cyclin B2 expression. Two peaks of gene expression activity were observed. One was transient, limited, and located immediately before and at the onset of cyclin B2 expression in the early proliferative zone. The other was generally much more pronounced and was located in the early hypertrophic zone. The upregulation of expression of COL2A1, its transcriptional activator Sox9, osteocalcin, MMP-13, and TGFbeta2 was observed immediately before and at the onset of cyclin B2 expression and also in the hypertrophic zones. The upregulation of COL10A1, Cbfa1, MMP-9, TGFbeta-1, and Ihh gene expression was associated exclusively with the terminal differentiation of chondrocytes at the time of mineral formation in the extracellular matrix. In contrast, bFGF and PTHrP expression was observed in association with the onset of cyclin B2 expression and hypertrophy. This initial cluster of gene expression associated predominantly with matrix assembly and onset of cell proliferation is therefore characterized by expression of regulatory molecules distinct from those involved at hypertrophy. Together these results identify separate phases of coordinated gene expression associated with the development of the physis in endochondral bone formation.