Percutaneous nocturnal oximetry (PNO) is useful to screen respiratory function in amyotrophic lateral sclerosis (ALS). PNO recordings of some patients disclose a periodical pattern of O(2) desaturation (PP), whose significance is unknown. We aimed to characterize PP pattern, and we used a prospective study enrolling 261 consecutive ALS patients. Clinical, pulmonary and neurophysiological tests performed included: ALS functional rating scale, forced vital capacity (FVC), maximal inspiratory pressure (PImax), mouth occlusion pressure (MOP), phrenic nerve motor response, needle electromyography of the diaphragm, PNO, and sleep study. A total of 837 PNO recordings were analysed (3.2 recordings/patient) and 45 patients showed typical PP (17.2%). Four were excluded, 13 had normal diaphragm (group 1, G1), and in 28 the diaphragm was abnormal (G2). The two groups were comparable, apart from respiratory score, FVC and PImax which were lower in G2. In G1, REM sleep was absent and hypoventilation occurred at slow-wave sleep. Five patients in G1 were very spastic, had low MOP/FVC and a short survival. This study identified a subgroup of ALS patients (G1) with marked signs of upper motor neuron lesion, strong respiratory muscles, PP, low MOP/FVC ratio and poor prognosis. We speculate that they have a central respiratory dysfunction and deserve special care.