Children with gastroesophageal reflux often suffer from chronic, severe lung damage and recurrent infections. The mechanisms may involve reflux induced lung injury with alterations of the surfactant proteins (SP) SP-A and SP-D, which bind specifically to various microbes and increase their elimination by granular leukocytes and macrophages. In 20 children with gastroesophageal reflux disease (GERD) the bronchoalveolar lavage content and macromolecular organization of SP-A and SP-D was determined by enzyme linked immunosorbent assay and gel chromatography. For comparison, lavages from 17 children without respiratory diseases were investigated. Both, SP-A and SP-D were significantly reduced in children with GERD-median (25, 75 percentiles) SP-A: 362 (169, 494) ng/ml versus 867 (656, 1,761) in control subjects and SP-D: 174 (73, 456) ng/ml versus 518 (295, 748) ng/ml in control subjects. The more active, higher molecular weight oligomers of SP-A and especially those of SP-D were diminished, whereas the smaller sized forms of SP-D were markedly increased. In children with GERD, significantly reduced amounts of SP-A and SP-D and an altered structural organization of the surfactant protein oligomers were demonstrated. Such impairments of central components of the innate host defense system may contribute to the pathogenesis of the chronic lung disease commonly observed in these children.