A small portion of cellular glycogen is transported to and degraded in lysosomes by acid ␣-glucosidase (GAA) in mammals, but it is unclear why and how glycogen is transported to the lysosomes. Stbd1 has recently been proposed to participate in glycogen trafficking to lysosomes. However, our previous study demonstrated that knockdown of Stbd1 in GAA knockout mice did not alter lysosomal glycogen storage in skeletal muscles. To further determine whether Stbd1 participates in glycogen transport to lysosomes, we generated GAA/Stbd1 double knock-out mice. In fasted double knock-out mice, glycogen accumulation in skeletal and cardiac muscles was not affected, but glycogen content in liver was reduced by nearly 73% at 3 months of age and by 60% at 13 months as compared with GAA knock-out mice, indicating that the transport of glycogen to lysosomes was suppressed in liver by the loss of Stbd1. Exogenous expression of human Stbd1 in double knock-out mice restored the liver lysosomal glycogen content to the level of GAA knock-out mice, as did a mutant lacking the Atg8 family interacting motif (AIM) and another mutant that contains only the N-terminal 24 hydrophobic segment and the C-terminal starch binding domain (CBM20) interlinked by an HA tag. Our results demonstrate that Stbd1 plays a dominant role in glycogen transport to lysosomes in liver and that the N-terminal transmembrane region and the C-terminal CBM20 domain are critical for this function.Liver and muscle are the two primary sites for glycogen metabolism in mammals. Glycogen is synthesized and mostly degraded in the cytoplasm, but a small percentage of glycogen is transported into the lysosomes and hydrolyzed by the enzyme acid ␣-glucosidase (GAA) 3 (1-3). Deficiency of GAA causes Pompe disease (glycogen storage disease type II), resulting in a progressive lysosomal glycogen accumulation and dysfunction in cardiac and skeletal muscle and other tissues (4 -6). Enzyme replacement therapy with recombinant human GAA is the only available therapy for this disorder to have remarkable success, but it also has significant limitations such as high titer antibody formation and difficulties in delivering the therapeutic protein to skeletal muscle tissues (7-11). A conceivable alternative way to treat Pompe disease would be to block the transport of cytoplasmic glycogen to the lysosomes. Thus, understanding how glycogen enters the lysosome is a critical step in finding new therapeutic targets for Pompe disease. It has been demonstrated that conventional autophagy (macroautophagy) plays an important role in the transport of glycogen to lysosomes in skeletal muscle (12). Specifically, knock-out of an autophagy key gene Atg7 resulted in a decrease of glycogen content by 50 -60% in skeletal muscles of GAA knock-out mice (12). This suggests that other routes exist for glycogen transport to lysosomes. In recent studies, starch binding domain-containing protein 1 (Stbd1) has gained attention for its potential involvement in glycogen transport. The Stbd1 protein contains a putat...