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Globotriaosylsphingosine (lyso Gb3) is considered as one of the biomarkers for Fabry disease. A rapid and simple UPLC-MS/MS method was developed for the determination of reliable biomarker, lyso Gb3. Total analytical procedure takes only 15 min including sample preparation and MS/MS analysis. Limit of detection was 0.85 ng/ml (S/N=3). The calibration curve was linear over the range of 2.0~400.0 ng/ml (R2=0.9999). Inter-day and intra-day assay accuracy were 93.4~100.6% (RSD, 0.6~6.0%) and 97.5~100.7% (RSD, 3.6~5.2%). Absolute recoveries of 97.6~98.6 showed excellence of a new analytical method. The method was applied to human and mice urines, proved the suitability for the quantification of lyso-Gb3 for screening, diagnosis and therapeutic monitoring of Fabry disease patients.