To analyze the physiologic effects and tolerance of mechanical insufflation-exsufflation (MI-E) by means of mechanical cough assistance (Cough Assist; JH Emerson Company; Cambridge, MA) for children with neuromuscular disease. Prospective clinical trial. Physiology laboratory of a pediatric pulmonary department of a university hospital. Seventeen children with Duchenne muscular dystrophy (n = 4), spinal muscular atrophy (n = 4), or other congenital myopathy (n = 9) who were in a stable state. Pressures of 15, 30, and 40 cm H(2)O were cycled to each patient, with 2 s for insufflation and 3 s for exsufflation. One application consisted of six cycles at each pressure for a total of three applications. Airway pressure and airflow were measured during every application. Breathing pattern, vital capacity (VC), sniff nasal inspiratory pressure (SNIP), peak expiratory flow (PEF), and respiratory comfort were evaluated at baseline and after each application. The tolerance of the patients was excellent, with a significant increase in the respiratory comfort score in all of the patients (p = 0.02). Expired volume during the MI-E application increased significantly to reach twice the VC at 40 cm H(2)O. Mean and maximal inspiratory and expiratory flows increased in a pressure-dependent manner. Breathing pattern did not change after the MI-E applications and pulse oximetric saturation remained stable within normal values, but the mean end-tidal carbon dioxide pressure decreased significantly. VC did not change, but the mean SNIP and PEF improved significantly after MI-E applications. Our results confirm the good tolerance and physiologic short-term benefit of the MI-E in children with neuromuscular disease who were in a stable state.