Understanding the rich complement of sugar chains found in cellular membranes is impeded by the complexity of cell types and membrane diversity. To overcome this, we have analyzed the N-linked sugar chain composition of the glycoproteins of CNS myelin, an elaboration of the plasma membranes of oligodendrocytes (OLs) that result in a multilamellar wrapping of neuronal axons, facilitating nerve conduction with dramatic savings of space and energy. Due to an usually high lipid to protein ratio, myelin can be separated readily from other heavier membranes on sucrose gradients and further fractionated into subdomains related to myelin structure and function, including compact myelin and myelin-associated axolemmal membrane (Menon et al. 2003). We analyzed these fractions for N-linked sugar chains, using 2D HPLC following hydrazinolysis and pyridylamination. Our results indicate that compared with total brain homogenate, the amount of N-glycans is 1.3-fold higher in the myelin-associated axolemmal membranes, but it is 0.5-fold less in CM. M5 [Man alpha 1-3((Man alpha 1-3)(Man alpha 1-6)Man alpha 1-6)Man beta 1-4GlcNAc beta 1-4GlcNAc] is the most abundant sugar chain in total brain homogenate, compact myelin, and myelin-associated axolemma, constituting similar to 20% of sugar chains. Although the types of sugar chains are similar among the fractions, their expression levels vary significantly. In addition to high mannose type oligosaccharides, the core fucosylated, biantennary N-glycans with bisecting N-acetylglucosamine (GlcNAc) residue, A2G1(3)FB [Gal beta 1-4GlcNAc beta 1-2Man alpha 1-3(GlcNAc beta 1-2Man alpha 1-6)(GlcNAc beta 1-4)Man beta 1-4GlcNAc beta 1-4(Fuc alpha 1-6)GlcNAc], A2G1(6)FB [GlcNAc beta 1-2Man alpha 1-3(Gal beta 1-4GlcNAc beta 1-2Man alpha 1-6)(GlcNAc beta 1-4)Man beta 1-4GlcNAc beta 1-4 (Fuc alpha 1-6)GlcNAc] and BA-1 [Man alpha 1-3(GlcNAc beta 1-2Man alpha 1-6)(GlcNAc beta 1-4)Man beta 1-4GlcNAc beta 1-4(Fuc alpha 1-6)GlcNAc], and A1(6)G0F [Man alpha 1-3(GlcNAc beta 1-2Man alpha 1-6)Man beta 1-4GlcNAc beta 1-4(Fuc alpha 1-6) GlcNAc] are also present in relatively large proportions in compact myelin. We suggest that these differences may be related to myelin-axolemmal function.