A recent physiological study established that hindlimb unloading of rats at 3 and 7 weeks inhibits healing of injured ligaments resulting in a badly aligned discontinuous collagen matrix. Using tissue from these rats we focused on the 3-week time point employing microarray analysis to identify what cellular processes or lack of processes could account for these observed deficiencies. We used the Affymetrix RG_U34A GeneChip and performed image analysis with Microarray Suite 5.0. For normalization we used the MAS global normalization protocol with a default target mean signal of 500. Gene expression in medial collateral ligament tissue under 4 different treatment conditions was measured: loaded control loaded wound healing unloaded control and unloaded wound healing. From our results it appears that unloaded tissue lags behind loaded tissue in its progression through the healing process and at 3 weeks is still engaged in the proliferative phase whereas loaded tissue is actively remodeling its collagen matrix.