Background Fabry disease is a complex, multisystemic and clinically heterogeneous disease, with elevated excretion of globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3) accumulating in biological fluids caused by deficiency of the enzyme, lysosomal α-galactosidase A. Our aims were to propose a tandem mass spectrometry fragmentation mechanism for lyso-Gb3, to develop and validate a simple, and robust methodology for the measurement of plasma lyso-Gb3 using LC–MS/MS in large Fabry cohorts and in controls. Response to treatment was also evaluated.