Our results demonstrate the feasibility of the metabolomics-based approach and provide a deeper understanding of FKRP-related dystroglycanopathies that can be helpful in identifying biomarkers of disease progression, distinguishing molecular markers and targets for therapeutic intervention, as well as predicting long-term, treatment-related side effects. Here, FKRP is linked to neuromuscular disease caused by qualitative or quantitative defects of alpha-dystroglycan.