Mammalian cells produce many glycoproteins, i.e., proteins with covalently attached sugar chains. Recent advances in glycobiology have revealed the importance of sugar chains as biosignals for multi-cellular organisms including cell-cell communication, intracellular signaling, protein folding, and targeting of proteins within cells. The O-mannosyl linkage, which used to be considered specific to yeast, has recently been found in mammals. One of the best known O-mannosyl-modified glycoproteins is alpha-dystroglycan, which is a central component of the dystrophin-glycoprotein complex isolated from skeletal muscle membranes. We have identified and characterized a glycosyltransferase, UDP-N-acetylglucosamine: protein O-mannose beta1,2-N-acetylglucosaminyltransferase (POMGnT1), 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). MEB is an autosomal recessive disorder characterized by congenital muscular dystrophy, ocular abnormalities and brain malformation (type II lissencephaly). Moreover, recent data suggest that aberrant protein glycosylation of alpha-dystroglycan is the primary cause of some forms of congenital muscular dystrophy. Here we review new insights into the glycobiology of muscular dystrophy and neuronal migration disorder.