Abstract: To understand the pathogenesis of PTA we studied the gene expression profiles of synovial cells of knee using gene chip analysis. PTA was induced by transection of the Anterior Cruciate Ligament (ACL) of left knee in 3 piglets. After sacrificing the piglet at 8 weeks, synovial cells were used for gene expression profiling using Affimetrix GeneChip. Affimetrix GeneChip Operating Software and Robust Multi-array Analysis (RMA) were used to identify differentially expressed genes. Expressions of selected genes were verified by RT-PCR. Histopathologic examination at 8 weeks showed overt chronic inflammation indicating the development of PTA. Through genome analyses it was observed that 87 known genes were up-regulated and 76 known genes were down regulated. By analyzing gene expression, we found differential expression of genes related to inflammatory and immune response, lipid binding, cell adhesion, growth activity and muscle development. Some of the important genes related to inflammatory and immune response are FAS, MCP-1, IL-18, IL-1α, IL-6, IL-7, OAS1, TLR4, MX2. RT-PCR result has confirmed the expression of selected genes (IL 6, IL 18, FABP 4, LPL and PLTP) in total RNA isolated from synovial cells. The genome analysis of synovial cells provided us new candidate molecules related to inflammation and immunity which may be useful to understand the pathogenesis of PTA.