Glycosaminoglycans (GAGs) were recovered from human cerebral spinal fluid (CSF) and after their conversion to disaccharides using polysaccharide lyases were analyzed by liquid chromatography tandem mass spectrometry using multiple reaction monitoring. CSF showed ng/mL levels of heparan sulfate, chondroitin sulfates and hyaluronan. The amounts and disaccharide composition of these GAGs differed from those found in human plasma. This approach may offer a new method for the discovery of biomarkers for diseases of the central nervous system. Glycosaminoglycans (GAGs) are linear and anionic polysaccharides, populating the cell surface and extracellular matrix, which are biosynthesized in the Golgi or at the cell membrane [1]. GAGs perform a wide spectrum of important biological functions in development, homeostasis, and disease, ranging from controlling cell-cell interactions, cell signaling, cell proliferation and interact with many different proteins [2][3][4][5]. When classified by their core, GAGs can be divided into four major families: heparan sulfate/heparin (HS/ HP), chondroitin sulfate/dermatan sulfate (CS/DS), keratan sulfate (KS) and hyaluronan (HA) based on their disaccharide (dp2) repeating units comprising their backbone structure. These units consist of an amino sugar, either N-acetyl-D-glucosamine (D-GlcNAc) or Nacetyl-D-galactosamine (D-GalNAc), and either an uronic acid, D-glucuronic (D-GlcA) or Liduronic acid (L-IdoA), or galactose in the case of KS. The linkage positions and