Mechanisms of epithelial renewal in the alveolar compartment remain incompletely understood. To this end, we aimed to characterize alveolar progenitors. Single-cell RNA-seq (scRNA-seq) analysis of the HTII-280 positive and HTII-280+ /EpCAM+populations from total 6 donors from periferal tissue was performed, and analysis revealed subclusters enriched for stem cell signature genes. We found that these alveolar progenitors in organoid culture in vitro show phenotypic lineage plasticity as they can yield alveolar or bronchial cell type progeny. The direction of the differentiation is dependent on the presence of the GSK-3β inhibitor, CHIR99021. By RNA-seq analysis of GSK-3 βknockdown organoids, we identify additional functional candidate target genes and pathways which contribute to alveolar differentiation independent of Wnt signaling Overall design: Human peripheral lung tissue resident HTII-280+ , and HTII-280+/Epcam+cells were analyzed by single-cell RNA sequencing (scRNA-seq). Organoid forming and differentiation capacity was tested in different signaling environments, and phenotype was characterized by scRNA-seq, confocal imaging, electron microscopy, qPCR, and immunoblotting. ShGSK3β organoids were generated by lentiviral tansduction of 2 different hairpins against GSK 3β and control vector The validity of organoids as an infection model for influenza virus (IAV) was established in comparison to human ex vivo lung tissue. Analysis code is available from https://github.com/bihealth/hoffmann_et_al_bronchioalveolar_organoids >>>Submitter states that raw data are unavailable due to patient privacy concerns<<<