Sleep related arterial oxygen desaturation has been described in clinically stable young adults with cystic fibrosis. The incidence and severity of nocturnal oxygen desaturation in children during infective exacerbations and the changes that occur with treatment were examined. Forty five children with proved cystic fibrosis, median age 8.9 years, admitted to the Regional Cystic Fibrosis Unit underwent clinical evaluation, spirometry, and measurement of peak flow and nocturnal oxygen saturation on admission and after 10 days' treatment. There was a significant improvement in all the above measurements, with the averaged overnight saturation changing from a mean (SD) 92.7 (2.7)% to 94.3 (2.0)%, mean (SE) difference 1.58 (0.37). The time spent with a saturation 4% or more below their clinic value showed a marked improvement from 122 (152) minutes on the first night to 21 (30.7) on the second, mean (SE) difference 101 (22.4). Eight young children could not perform pulmonary function tests, all desaturated on the admission night. Nocturnal hypoxaemia is a common finding in young cystic fibrosis patients during infective exacerbations but improves with treatment. Overnight oximetry is simple to perform, well tolerated, and identifies patients with marked nocturnal desaturation.