Abstract Background Dysregulation of the airway epithelium contributes to recurrent wheezing and asthma and may have developmental origins. Here, we investigated the relationship between the placental amniotic and nasal epithelial methylation landscapes to determine whether amniotic epithelium provides insight into fetal programming of respiratory tissue. Methods We conducted high-throughput target-capture DNA methylation sequencing of 84 matched pairs of placental amniotic and neonatal nasal brushings samples within the Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) cohort. Comparative analysis of tissue-specific methylation profiles, and conservation of methylation changes associated with gestational exposures (maternal smoking and maternal asthma), was explored. Results Between amniotic and nasal tissues, we identified 4,897 differentially methylated regions (FDR ≤ 0.05 and log 2 FC ≥ |0.2|) that were generally hypermethylated in the nasal epithelium. Despite these extensive tissue-specific differences, filtering for loci with non-significant differential methylation (FDR ≥ 0.1) revealed 1,493,976 CpG loci (∼20% of the measured methylome) with highly concordant methylation ratios levels between tissues (Pearson’s R ≥ 0.8). These loci included genes crucial to epithelial and lung development. Within these conserved regions, associations with maternal asthma and prenatal smoking were consistently represented in both tissues. Conclusions The conserved methylome signatures support the use of amniotic tissue as a valuable tissue for investigating the developmental programming of airway vulnerability, potentially leading to early risk stratification and targeted interventions for childhood asthma. Sources of support This work was supported by grants from the National Health and Medical Research Council of Australia (APP1157548), Department of Health (Western Australia)-Future Health Research and Innovation Fund (2020, 2021, 2022). S.M.S. is supported by an NHMRC Investigator Grant (NHMRC2007725). P.A-R. received funding from the Google Cloud Education Program, a Telethon Kids Institute Theme Collaboration Award grant (PR030564), the Branchi Family Foundation, and a Future Health Research and Innovation (FHRI) Fellowship by the Department of Health (IF2024-25/1), Government of Western Australia. T.I. is supported through the Channel 7 Telethon Trust, Stan Perron Charitable Foundation People Fellowship and previously supported by the Future Health Research Innovation Fund (FHRIF 2020-2023) and Imogen Miranda Suleski Fellowship. A.K is a Rothwell Family Fellow and D.G.H. is a Stan Perron/Perth Children’s Hospital Foundation (PCHF) Fellow. D.M. is supported by FHRIF. A.B. is supported by the NIH (R21 AI176305-01A1, R01AI099108-11A1). The ORIGINS birth cohort has received core funding support from the Paul Ramsay Foundation and the Commonwealth Government of Australia through the Channel 7 Telethon Trust. Substantial in-kind support has been provided by The Kids Research Institute Australia and Joondalup Health Campus.