Topographical cartilage variation across the knee joint has been previously reported, but there is only limited information on such gene expression profiles. Articular chondrocytes from eight different topographical regions of bovine knee joints were seeded within three-dimensional scaffolds and further cultured under static conditions (unloaded control group) or subjected to an artificial joint environment within a bioreactor (loaded group). Constructs were analyzed for glycosaminoglycan (GAG), DNA, and expression of Collagen-1,-2,-10, Aggrecan, COMP, Sox9, PRG-4, PTHrp, and MMP-1,-3,-13 mRNA after 2 weeks of in vitro culture. Exclusively among loaded constructs the overall GAG production was significantly different between regions. Patella chondrocytes had overall highest, and cells from the femoral notch had overall lowest GAG/DNA under loaded conditions. Gene expression was significantly different between regions for all targets except for Sox9, PRG-4, and PTHrp among controls and with the exception of Aggrecan, Sox9, and PTHrp among loaded samples. Under mechanical stimulation Collagen-1,-2 and Aggrecan was highest at the patello-femoral joint, whereas it was lowest at typical cartilage biopsy regions. There is a clear topographical variation among distinct regions across the knee joint for gene and matrix expression profiles under static and foremost under dynamic conditions.