One issue with a number of publications on enzyme replacement therapy in Pompe disease is with the glycogen determination on mouse tissues. Glycogen is a polysaccharide consisting of different sizes of particles. In the analysis of tissues, if the boiled tissue homogenate is centrifuged before the amyloglucosidase incubation to release glucose from glycogen, it is possible that glycogen may be precipitated along with proteins. The centrifugation steps used in glycogen determinations in publications varies from about 300 × g to 18,000 × g. Therefore, clearly all of the work is not measuring the same component. The problem with the commercial kits is that their protocol involves the centrifugation of the boiled homogenate, usually up to 18,000 x g, for 5 to 10 minutes and the supernatant is used for the amyloglucosidase incubation. The commercial kits specify centrifugation to avoid particulate matter in the 96 well plates used for the assay. Also a number of papers describe glycogen determination of glucose released by amyloglucosidase without giving details but often citing a reference. Unfortunately, the reference cited does not always mention the details either. Therefore, the result is a large number of published papers in which the complete glycogen procedure is not described making it impossible for the work to be reproduced. Given the nature of glycogen and boiling extracts before centrifugation and using only the supernatant for the degradation of glycogen and determination of glucose released does not represent the true glycogen content of the tissue. This problem is present in a large number of papers on a number of subjects other than the papers on ERT and Pompe disease. Based on citations listed on company web sites and the papers with lack of detail it is likely that the number of publications with the problem may number in the hundreds.