Inflammation is a complex, biologic event that aims to protect and repair tissue. Previous studies suggest that inflammation is critical to induce a healing response following acute injury; however, whether similar inflammatory responses occur as a result of beneficial, non-injurious loading is unknown. The objective of this study was to screen for alterations in a subset of inflammatory and extracellular matrix genes to identify the responses of rat supraspinatus tendon and muscle to a known, non-injurious loading condition. We sought to define how a subset of genes representative of specific inflammation and matrix turnover pathways is altered in supraspinatus tendon and muscle 1) acutely following a single loading bout and 2) chronically following repeated loading bouts. In this study, Sprague-Dawley rats in the acute group ran a single bout of non-injurious exercise on a flat treadmill (10 m/min, 1 hour) and were sacrificed 12 or 24 hours after. Rats in the chronic group ran 5 days/wk for 1 or 8 weeks. A control group maintained normal cage activity. Supraspinatus muscle and tendon were harvested for RNA extractions, and a custom Panomics QuantiGene 2.0 multiplex assay was used to detect 48 target and 3 housekeeping genes. Muscle/tendon and acute/chronic groups had distinct gene expression. Components of the arachidonic acid cascade and matrix metalloproteinases and their inhibitors were altered with acute and chronic exercise. Collagen expression increased. Using a previously validated model of non-injurious exercise, we have shown that supraspinatus tendon and muscle respond to acute and chronic exercise by regulating inflammatory- and matrix turnover-related genes, suggesting that these pathways are involved in the beneficial adaptations to exercise.