Considering the clinical heterogeneity of patients with a late onset form of Pompe disease, we clearly need reliable quantitative surrogate markers allowing to accurately determine the effects of enzyme replacement therapy (ERT). In the present study, we investigated, using quantitative MRI and usual clinical tests, the effects ERT in three patients with a late onset form of the Pompe disease. Data were compared before and throughout a 4-year ERT period. MR images were processed using a robust automatic segmentation tool in order to quantify muscle, subcutaneous adipose tissue and intramuscular adipose tissue. Motor (6-min walking test (6MWT), manual motor testing, Motor Function Measure scale) and respiratory function (vital capacity, (FVC)) were investigated once a year. Clinical tests remained stable in patient 2 and worsened in patient 1. In patient 3, the 6MWT improved whereas the FVC remained stable. In two patients (patient 1 and 2), the rate of intramuscular infiltration was substantially slowed throughout the treatment period whereas it increased in patient 3 who required nocturnal ventilation. We demonstrated a variable effect of the ERT while clinical and MRI results were not directly related. The quantitative MRI kinetic index we selected might be of interest for further investigations in a larger group which are warranted in order to clearly delineate the effects of ERT in adult patients with Pompe disease.