Mesenchymal stems cells have a demonstrated ability to differentiate into muscle, bone, and fat. Determining whether these same cells have the ability to differentiate into tendon-like fibroblasts has been hampered by the lack of specific tendon cell marker genes. In order to identify molecular markers of mature tendon, expression profiling was used to identify genes expressed in adult rat and human tendon tissue compared to other musculoskeletal tissues. Using this technique, approximately 1,600 transcripts appeared to be selectively expressed in rat tendon tissue and approximately 300 transcripts appeared to be selectively expressed in human tendon tissue, with approximately 20 genes selectively expressed in both human and rat tendon tissue. Of these common tendon-selective genes, thrombospon-din-4 (THBS4) and tenomodulin (TNMD) were found to have the highest tendon-selective expression compared to other tissues examined. Interestingly, expression of these tendon-selective genes, which are present in primary tendon fibroblasts, is lost when these cells are placed in two-dimensional culture systems. In conclusion, this study has defined a set of tendon-selective genes present in both adult rat and human tendons. Identification of tendon-selective genes provides potential molecular tools to facilitate a better understanding of tendon development and tendon repair.