Adult-onset glycogen storage disease type II (GSD II) (McKusick 232300) is a progressive disabling myopathy. At present there is no treatment of proven clinical efficacy. Enzyme replacement therapy may in the future provide benefit but it will be costly and is not yet freely available. L-Alanine, a simple and relatively cheap therapy, has been shown to reduce protein degradation in GSD II patients but has not previously been assessed for clinical benefit in a controlled study. In this study L-alanine was assessed in a double blind, placebo-controlled, crossover n = 1 study. Assessments consisted of spirometry, cardiopulmonary exercise testing, quality of life measurements, biochemical markers and assessment by the criterion 4-component model of body composition. Alanine therapy was associated with a 15% gain in total body protein. However, the patient showed no functional improvement and reported feeling worse after treatment. Further controlled studies in a small group may be warranted, but not widespread use of this therapy.