A capillary zone electrophoresis-laser induced fluorescence detection (CZE-LIF) method was developed for the simultaneous analysis of disaccharides derived from heparan sulfate, chondroitin sulfate/dermatan sulfate, hyaluronan and keratan sulfate. Glycosaminoglycans (GAGs) were first depolymerized with the mixture of GAG lyases (heparinase I, II, III and chondroitinase ABC and chondroitinase AC II) and GAG endohydrolase (keratinase II) and the resulting disaccharides were derivatized by reductive amination with 2-aminoacridone. Nineteen fluorescently labeled disaccharides were separated using 50 mM phosphate buffer (pH 3.3) under reversed polarity at 25 kV. Using these conditions, all the disaccharides examined were baseline-separated in less then 25 min. This CZE-LIF method gave good reproducibility both migration time (≤ 1.03% for intra-day and ≤ 4.4% for inter-day) and the peak area values (≤ 5.6% for intra- and ≤ 8.69% for inter-day). This CZE-LIF method was used for profiling and quantification of GAG derivative disaccharides in bovine cornea. The results shows that the current CZE-LIF method offers fast, simple, sensitive, reproducible determination of disaccharides derived from total GAGs in a single run.