Introduction Little is known about early predictors of later cystic fibrosis (CF) structural lung disease. This study examined early predictors of progressive structural lung abnormalities in children who completed the Australasian CF Bronchoalveolar Lavage (ACFBAL) clinical trial at age 5-years and participated in an observational follow-up study (CF-FAB). Methods Eight Australian and New Zealand CF centres participated in CF-FAB and provided follow-up chest computed-tomography (CT) scans for children who had completed the ACFBAL study with baseline scans at age 5-years. CT-scans were annotated using PRAGMA-CF scoring. Ordinal regression analysis and linear regression were used to investigate associations between PRAGMA-CF outcomes at follow-up and variables measured during the ACFBAL study. Results Ninety-nine of 157 ACFBAL children (mean age 13-years, standard deviation 1.5) participated in the CF-FAB study. The probability of bronchiectasis at follow-up increased with airway disease severity on the baseline CT-scan. In multiple regression (retaining factors at p<0.05) the extent of bronchiectasis at follow-up was associated with baseline atelectasis (odds ratio (OR)7.2; 95% confidence interval (CI) 2.4, 22; P≤ 0.001), bronchoalveolar lavage (BAL) log2 interleukin (IL)-8 (OR 1.2 95%CI 1.05, 1.5; p=0.010) and body mass index z-score (OR 0.49, 95%CI 0.24, 1.00; p=0.05) at age 5-years. Percent trapped air at follow-up was associated with BAL log2 IL-8 (coefficient 1.3, 95%CI 0.57, 2.1; p<0.001) at age 5-years. Conclusions The extent of airway disease, atelectasis, airway inflammation, and poor nutritional status in early childhood are risk-factors for progressive structural lung disease in adolescence.