Introduction. Through muscle biopsy we can observe the formation of vacuoles that alter the structure of cells and tissues in Pompe's disease. The presence of these vacuoles varies as the disease progresses, relating to the broad clinical spectrum presented by the disease. Objectives. After confirming the disease, examine the possibility of diagnosing or excluding the diagnosis of Pompe's disease through the vacuolar characteristics presented. Method. Analysis of the muscle biopsy material of selected patients at the Neuromuscular Diseases Investigation Clinic at the Federal University of São Paulo. Through staining and histochemical techniques, a comparative study of the histological characteristics found was performed. Results. Thirty-three biopsies had the diagnosis of Pompe's disease confirmed, being 13 women and 20 men. Of this group, 23 received the diagnosis when they were 18 years old or more, and 10 received the diagnosis under the age of 18 years. Delimiting membrane and subsarcolemal location were the main vacuolar characteristic found, manifesting in 86.6% of the studied cases. Integration between the vacuole membranes was observed in 62.5% of the cases. We also found necrosis, replacement of muscle tissue by connective or adipose tissue, increased mitochondrial activity and absence of predominance in one type of fiber. Conclusion. Muscle biopsy allows to analyze a series of peculiarities presented by vacuoles in Pompe's Disease and, thus, it proves to be a sure technique, allowing to reach a quick conclusion and to identify determining factors for the clinical conduct and maintenance of quality of life of the patient with Pompe's disease.