Late onset Pompe disease (LOPD) is a rare muscle disorder often characterized, along the disease course, by severe respiratory failure. We describe herein respiratory muscles and lung abnormalities in LOPD patients using MR imaging and CT examinations correlated to pulmonary function tests. Ten LOPD patients were studied: 6 with a limb-girdle muscle weakness, 1 with myalgias, 2 with exertional dyspnoea and 1 with isolated hyperckemia. Respiratory function was measured using forced vital capacity (FVC) in both upright and supine positions, maximal inspiratory pressure (MIP), maximal expiratory pressure (MEP) and peak cough flow (PCF) tests. The involvement (atrophy) of diaphragms, abdominal respiratory muscles and intercostal muscles was ranked by CT and MRI examinations using appropriate scales. Height of lungs and band-like atelectasis presence were also recorded. Seven out of 10 patients showed a functional diaphragmatic weakness (FVC drop percentage >25%). In 8 out of 10 patients, involvement of both diaphragms and of other respiratory muscles was seen. The mean height of lungs in patients was significantly reduced when compared to a control group. Marked elevation of the diaphragms (lung height < 15 cm) was also seen in 6 patients. Multiple unilateral or bilateral band-like atelectasis were found in 4 patients. Statistically significant correlations were found between diaphragm atrophy grading, evaluated by MRI and CT, and FVC in supine position, FVC drop percentage passing from upright to supine position, PCF and MIP. Our data showed that diaphragm atrophy, often associated to reduced lung height and band-like atelectasis, can be considered the CT-MRI hallmark of respiratory insufficiency in LOPD patients. Early recognition of respiratory muscles involvement, using imaging data, could allow an early start of enzyme replacement therapy (ERT) in LOPD.