The diagnosis of Pompe disease (acid maltase deficiency, glycogen storage disease type II) in children and adults can be challenging because of the heterogeneous clinical presentation and considerable overlap of signs and symptoms found in other neuromuscular diseases. This review evaluates some of the methods used in the diagnosis and differential diagnosis of late-onset Pompe disease. Muscle biopsy is commonly used as an early diagnostic tool in the evaluation of muscle disease. However, experience has shown that relying solely on visualizing a periodic acid–Schiff–positive vacuolar myopathy to identify late-onset Pompe disease often leads to false-negative results and subsequent delays in identification and treatment of the disorder. Serum creatine kinase level can be normal or only mildly elevated in late-onset Pompe disease and is not very helpful alone to suggest the diagnosis, but in combination with proximal and axial weakness it may raise the suspicion for Pompe disease. A simple blood-based assay to measure the level of α-glucosidase activity is the optimal initial test for confirming or excluding Pompe disease. A timely and accurate diagnosis of late-onset Pompe disease likely will improve patient outcomes as care standards including enzyme replacement therapy can be applied and complications can be anticipated. Increased awareness of the clinical phenotype of Pompe disease is therefore warranted to expedite diagnostic screening for this condition with blood-based enzymatic assays.