Primary Ciliary Dyskinesia (PCD) is a genetic disease caused by gene mutations that alter cilia beating, including in the respiratory airways, resulting in impaired mucus clearance. We hypothesized that human induced pluripotent stem cells (iPSC) could help to restore bronchial cilia beating. Briefly, we differentiated genetically corrected iPSC into air-liquid interface bronchial epithelium (iALI) that can provide an unlimited source of cells for clinical interventions. We then tried to isolate from iALI cultures NKX2.1+ lung progenitors and p63+/KRT5+ basal cells, the main candidate cell types for lung regeneration. To this aim, we used two different engineered cell lines that express a fluorescent protein under the control of a transcription factor promoter (NKX2.1 and/or p63). However, we did not detect any specific fluorescence or just above background, presumably due to the high auto-fluorescence of differentiating bronchial progenitors. This prevented the use of these cell lines to prospectively select the target cells. We are currently using transcriptomic data to identify cell surface markers for magnetic cell sorting. A second issue is the best bronchial erosion method before cell therapy. In a preliminary experiment, we compared mechanical (scratch), chemical (SDS and CHAPS), and enzymatic (trypsin) erosion. The homogeneous detachment of the cells obtained with trypsin suggest that by enzymatic erosion is the best approach. In conclusion, our data underline the necessity i) to identify cell surface markers to isolate the best stem cell population from iALI cultures for cell therapy, and ii) to determine the best bronchial erosion strategy to promote cell engraftment.