To determine the effect of loading conditions on the length of primary cilia in tendon cells in situ, freshly harvested rat tail tendons were stress-deprived (SD) for up to 72 h, cyclically loaded at 3% strain at 0.17 Hz for 24 h, or SD for 24 h followed by cyclic loading (CL) for 24 h. Tendon sections were stained for tubulin, and cilia measured microscopically. In fresh control tendons, cilia length ranged from 0.6 to 2.0 µm with a mean length of 1.1 µm. Following SD, cilia demonstrated an increase (p < 0.001) in overall length at 24 h when compared to controls. Cilia length did not increase with time of SD (p = 0.329). Cilia in cyclically loaded tendons were shorter (p < 0.001) compared to all SD time periods, but were not different from 0 time controls (p = 0.472). CL for 24 h decreased cilia length in 24 h SD tendons (p < 0.001) to levels similar to those of fresh controls (p = 0.274). The results of this study demonstrate that SD resulted in an immediate and significant increase in the length of primary cilia of tendon cells, which can be reversed by cyclic tensile loading. This suggests that, as in other tissues, cilia length in tendon cells is affected by mechanical signaling from the extracellular matrix.