The O-mannosyl glycan is present in a limited number of glycoproteins of brain, nerve, and skeletal muscle. alpha-Dystroglycan is one of the O-mannosylated proteins and is a central component of the dystrophin-glycoprotein complex that has been shown to be related to the onset of muscular dystrophy. We have identified and characterized glycosyltransferases, protein O-mannose beta1,2-N-acetylglucosaminyltransferase (POMGnT1) and protein O-mannosyltransferase 1 (POMT1), involved in the biosynthesis of O-mannosyl glycans. We subsequently found that loss of function of the POMGnT1 gene is responsible for muscle-eye-brain disease (MEB). It has also been reported that the POMT1 gene is responsible for Walker-Warburg syndrome (WWS). MEB and WWS are autosomal recessive disorders characterized by congenital muscular dystrophies with neuronal migration disorders. Therefore, the ability to assay enzyme activities of mammalian O-mannosylation would facilitate progress in the identification of other O-mannosylated proteins, the elucidation of their functional roles, and the understanding of muscular dystrophies. This protocol describes assay methods for the mammalian POMT and POMGnT.