Tendinopathies are commonly attributable to accumulation of sub-rupture fatigue damage from repetitive use. Data is limited to late stage disease from patients undergoing surgery, motivating development of animal models, such as ones utilizing treadmill running or repetitive reaching, to investigate the progression of tendinopathies. We developed an in vivo model using the rat patellar tendon that allows control of the loading directly applied to the tendon. This manuscript discusses the response of tendons to fatigue loading and applications of our model. Briefly, the fatigue life of the tendon was used to define low, moderate and high levels of fatigue loading. Morphological assessment showed a progression from mild kinks to fiber disruption, for low to high level fatigue loading. Collagen expression, 1 and 3 days post loading, showed more modest changes for low and moderate than high level fatigue loading. Protein and mRNA expression of Ineterleukin-1β and MMP-13 were upregulated for moderate but not low level fatigue loading. Moderate level (7200 cycles) and 100 cycles of fatigue loading resulted in a catabolic and anabolic molecular profile respectively, at both 1 and 7 days post loading. Results suggest unique mechanisms for different levels of fatigue loading that are distinct from laceration.