The activity of the AMP-activated protein kinase (AMPK) is central to the maintenance of both cellular and whole body energy homeostasis. AMPK functions as heterotrimer with the catalytic activity residing in the α-subunit and the γ and β-subunits performing regulatory functions. While the role of the γ-subunit in the allosteric binding of AMP has been established in recent years, the regulatory role of the β-subunit has remained elusive. The β-subunit has a C-terminal ASC domain required for interactions with both the α and γ- subunits. In addition to the ASC domain the N-terminus of the β-subunit has a 120 amino acid segment with strong homology to “N-isoamylase-like domain”. The latter are non-catalytic domains found in enzymes that metabolise the α1-6 glycosidic linkages of polysaccharides such as glycogen and starch. Previous work by this laboratory (1) and others (2) revealed that this domain is capable of binding to glycogen both in-vitro and in-vivo. This domain has subsequently been re-named the glycogen-binding domain (GBD). Glycogen is the main storage polysaccharide found in mammalian cells. It represents a plentiful source of glucose that is readily available for ATP generation. Glycogen molecules are large, heterogeneous, tree-like structures nucleated by a single glycogenin protein. Within the glycogen particle glucose molecules are linked by α1-4 glycosidic linkages with branches appearing every 10-12 glucose units via a α1-6 glycosidic link. In the study reported here we have found that glycogen can inhibit AMPK activity. Using the recombinant AMPK complex we have shown that the inhibitory effect of glycogen is blocked by mutation of two key tryptophan residues within the GBD. We have additionally shown that mutation of these two tryptophan residues within the isolated domain abolishes glycogen binding to the GBD. Attempts to define fragments of glycogen that bind to the GBD resulted in the discovery that AMPK interacts with and is inhibited by isomaltose. Isomaltose is a α1-6 linked disaccharide of glucose that mimics the branch-points of the glycogen particle. It is additionally reported that degradation of glycogen by phosphorylase to expose the branch-points increases the potency of AMPK inhibition, while chemically synthesised branched oligopolysaccharides have a similar effect. This work suggests the GBD of AMPK specifically recognises the branch-points of the glycogen particle with consequences for the regulation of the AMPK system. In this sense AMPK may therefore monitor the quality as well as the quantity of cellular glycogen.