Impaired glucose storage is a defect that contributes to peripheral insulin resistance in Type 2 Diabetes. This has been associated with mutations in the glycogen synthase gene. The aim of the present study was to examine the effects of deletion of the glycogen synthase (gys1) gene specifically in skeletal muscle on glucose metabolism, using an inducible Cre mouse system. Muscle specific MerCreMer mice were bred with gys1 floxed (Gyslox) mice to generate animals with a Gyslox+/+/Cre+/- (knockout) and Gyslox+/+/Cre-/- (control) genotype. At 10 weeks of age, mice were fed a specially formulated diet containing 1 mg/g tamoxifen or a matched chow control diet for up to seven weeks. Body weight was not different following tamoxifen treatment in either the control or gys1 knockout mice over the seven weeks. An oral glucose tolerance test (OGTT) and basal glucose turnover was performed at the end of diet treatment following a 6 hour fast. We found that compared to Gyslox+/+/Cre-/- control mice, the Gyslox+/+/Cre+/- knockout mice with >80% deletion of muscle gys1 were glucose intolerant (insulin AUC: control 67.6±4.4 vs gys1-ko 83.6±8.5 ng/mlx120min, P<0.05). Under basal conditions, the metabolic clearance rate of Gyslox+/+/Cre+/- knockout mice was significantly lower than Gyslox+/+/Cre-/- control mice (gys1-ko: 8.46±0.67 ml/min/kg vs control: 11.96±1.01 ml/min/kg P<0.05). Together our data demonstrate that an 80% reduction of gys1 in the skeletal muscle leads to a significant reduction in metabolic clearance rate and an overall intolerance to glucose.