BACKGROUND: Abnormalities of pulmonary function have been found in children with systemic lupus erythematosus (SLE) even in the absence of clinical or radiographic evidence of pulmonary involvement. It is unknown whether these abnormalities represent an early sign of progressive lung disease or whether they are associated with disease activity. METHODS: After a mean of 4.5 years, respiratory function (forced vital capacity (FVC) and single breath gas transfer factor (TLCO)) and disease activity were reexamined in 13 of 15 previously studied children with SLE. Disease activity was assessed by a validated index of SLE activity (SLE activity measure (SLAM)). RESULTS: In spite of the high prevalence of abnormalities of respiratory function at the baseline investigation, no chest radiographic abnormalities or overt clinical signs of lung disease were found at baseline, in the interval between the two investigations, or at the re-evaluation in any patient. From baseline to the second investigation the mean value of SLAM decreased and there was a trend toward an improvement in FVC and TLCO. TLCO was more severely impaired than FVC, being found as an isolated abnormality in a high percentage of patients (45% at baseline and 35% at follow up). There was a relationship between baseline TLCO and disease activity, expressed as a SLAM score. Moreover, there was a correlation between the changes in the SLAM score from baseline to the second investigation and the corresponding changes in the TLCO value, but not with the corresponding changes in the FVC value. CONCLUSIONS: In this series of patients the decrease in SLE activity from the first to the second investigation was associated with an improvement in pulmonary function. The presence of early isolated functional abnormalities was not associated with subsequent development of lung disease.