Faciscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant disorder with a characteristic distribution of weakness and variable severity. Prospective, longitudinal data on FSHD are essential for the design of therapeutic trials and in assessment of genetic heterogeneity. We enrolled 32 well-defined FSHD patients and 32 normal subjects in a natural history study of FSHD. All subjects underwent baseline quantitative muscle testing (QMT), manual muscle testing (MMT), and functional testing. QMT demonstrated substantial weakness in muscles usually spared in FSHD. Major right/left side-to-side differences in strength were documented but, unexpectedly, were not related to handedness. Using the QMT data on normal subjects, we developed regression models relating strength to age, gender, and height and used these models to standardize QMT measurements in FSHD patients, expressing them as the number of SDs from average normal performance. This model-based strategy should facilitate the construction of composite scores to describe the natural history of FSHD and could be useful for constructing sensitive measures of progression in other neuromuscular diseases.