Background: Multiple-breath washout (MBW) has been shown to detect early impairment of lung function in children with cystic fibrosis (CF). Nitrogen (N 2 ) or sulfur hexafluoride (SF 6 ) can be used as tracer gas for MBW. Recent data indicated higher lung clearance index (LCI) values measured with N 2 -MBW than concurrent SF 6 -MBW in older children and adults, however, a comparison in infants and younger children, as well as to other outcome measures of CF lung disease is pending. Methods: N 2 -and SF 6 -MBW were performed consecutively in 31 sedated infants and preschool children with CF (mean age, 2.3 ± 0.8 years) and 20 controls (mean age, 2.3 ± 1.1 years) using the Exhalyzer D system. Children with CF also underwent chest magnetic resonance imaging (MRI). Results: Mean difference (95% CI) in LCI between N 2 -and SF 6 -MBW was 1.1 ± 0.4 (0.9 to 1.3) in controls and 2.1 ± 1.9 (1.4 to 2.8) in CF. Agreement between N 2 -and SF 6 -LCI was poor in children with CF. N 2 -LCI and SF 6 -LCI correlated with MRI, however N 2 -LCI showed a higher concordance with MRI than SF 6 -LCI. The absolute difference between N 2 -and SF 6 -LCI values increased with the severity of CF lung disease as determined by MRI scores. Conclusion: N 2 -LCI values were higher than SF 6 -LCI values in infants and preschool children with CF and controls. Better concordance of N 2 -LCI than SF 6 -LCI with chest MRI scores point towards of a higher sensitivity of N 2 -LCI to detect early lung disease in children with CF.