Background: Congenital thoracic malformations (CTM) are rare lung lesions that are managed with surgical resection or active surveillance. The objective of this study was to comprehensively assess large and small airway function in children with CTM who underwent lobectomy in early life. We hypothesise that sensitive measures of lung function will demonstrate residual impairments in CTM compared to healthy children., Methods: Nitrogen lung clearance index (LCI), reactance and resistance (X5Hz and R5Hz), forced expiratory volume in 1 s and forced vital capacity (FEV1 and FVC) were prospectively measured in 10 children with CTM (mean age/SD: 7.6/1.3) who had undergone surgical resection in early life and in 17 healthy children (mean age/SD: 4.8/0.4). Total lung capacity (TLC) was also conducted in children older than 7 years of age with CTM (n = 8)., Results: Mean LCI was 8.0 (95% CI 7.5 to 8.5) in the CTM group and 7.3 (95% CI 7.0 to 7.6) in healthy children (p = 0.016). Mean X5Hz was -0.44kPa/l/s (95% CI -0.58 to -0.31) in the CTM group and -0.31kPa/l/s (95% CI -0.35 to -0.27) in healthy children (p = 0.02). Mean Z score for X5Hz was -2.11 (95% CI -3.59 to -0.63) in the CTM group and -0.11 (95% CI -0.55 to 0.33) in healthy children (p = 0.0008). Mean FEV1 was 1.21 L (95% CI 0.97 to 1.45) in the CTM group and 1.02 L (95% CI 0.90 to 1.15) in healthy children (p = 0.22). Mean % predicted FEV1 was 83% (95% CI 74 to 92) in the CTM group and 97% (95% CI 87 to 107) in healthy children (p < 0.05). Mean % predicted TLC in CTM children was 121.3% (95% CI 88.45 to 154.1). Mean LCI was inversely correlated with height z-scores in the CTM group (rs = -0.88, p = 0.002) but not in healthy children (rs = 0.22, p = 0.4)., Conclusions: Children with CTM have impaired lung function as demonstrated by the significant differences in LCI, reactance and FEV1 but not FVC, resistance and TLC. These findings may be of clinical relevance as ventilation inhomogeneities are closely correlated with somatic growth in this study.