Background:In-utero environment differences regarding inflammation, autophagy and remodelling may have effects on fetal lung development and respiratory morbidity in infants born to mothers with asthma in pregnancy. Aims:To compare levels of cord blood biomarkers in infants born to mothers with asthma in pregnancy (Breathing for Life Trial, BLT) and those born to non-asthmatic mothers (Basel-Bern Infant Lung Development (BILD) cohort, investigating markers linked to inflammation, autophagy, and remodeling, which also play a role in prenatal lung development. Additionally, to investigate whether those biomarkers are associated with infant lung function and bronchiolitis. Methods:Tobit regression was applied to analyse protein marker levels, linear regression for postnatal lung function at 4-6 weeks (tPTEF/tE%, minute ventilation, and lung volume FRC) and logistic regression for the prevalence of bronchiolitis hospitalisation in infancy. All models were adjusted for potential confounders. Results:Term infants born to asthmatic mothers (n=131 vs. n=614 non-asthmatic) had lower levels of MMP9 (? -0.67, p=0.009), IFN-? (? -0.77, p=0.002), and higher levels of p62 (? 1.15, p =0.03). p62 levels were inversely associated with tPTEF/tE (? -0.53, p=0.044) and minute ventilation (? -16.2, p=0.009) whilst MMP9 and IFN-? levels (? -1.27, p=0.032) with FRC. MMP9 was inversely associated with bronchiolitis hospitalisation in the first year of life (aOR 0.45, p=0.003). Conclusion: Supporting the hypothesis that an impaired intrauterine environment in asthmatic mothers affects infant health, remodelling and autophagy markers differed in their offspring compared to infants of healthy mothers. These markers were associated with differences in postantal lung function and bronchiolitis in infancy.