AbstractFabry disease (FD) is a lysosomal disorder caused by mutations leading to a deficient activity α‐galactosidase A with progressive and systemic accumulation of its substrates. Substrates deposition is related to tissue damage in FD, but the underlying molecular mechanisms remain not completely understood. DNA damage has been associated with disease progression in chronic diseases and was recently described in high levels in Fabry patients. Once renal complications are major morbidity causes in FD, we investigated the effects of the latest biomarker for FD – globotriaosylsphingosine (lyso‐Gb3) in a cultured renal lineage – human embryonic kidney cells (HEK‐293 T) – on DNA damage. In concentrations found in Fabry patients, lyso‐Gb3 induced DNA damage (by alkaline comet assay) with oxidative origin in purines and pyrimidines (by comet assay with endonucleases). These data provide new information about a deleterious effect of lyso‐Gb3 and could be useful to studies looking for new therapeutic strategies to FD.