INTRODUCTION: As we move toward planning for clinical trials in facioscapulohumeral muscular dystrophy (FSHD), a better understanding of the clinical relationship with morphological changes in FSHD muscle biopsies will be important for stratifying patients and understanding post-therapeutic changes in muscle. METHODS: We performed a prospective cross-sectional study of quadriceps muscle biopsies in 74 genetically confirmed FSHD participants (64 with FSHD type 1 and 10 with FSHD type 2). We compared a 12-point muscle pathology grade to genetic mutation, disease severity score, and quantitative myometry. RESULTS: Pathology grade had moderate correlations with genetic mutation (rho = -0.45, P < 0.001), clinical severity score (rho = 0.53, P < 0.001), disease duration (rho = 0.31, P = 0.03), and quantitative myometry (rho = -0.47, P < 0.001). We found no difference in the frequency of inflammation between FSHD types 1 and 2. CONCLUSIONS: The pathology grade of quadriceps muscle may be a useful marker of disease activity in FSHD, and it may have a role in stratification for future clinical trials.