Abstract Background The domestic pig is an excellent animal model to study human microbial diseases due to its similarity to humans in terms of anatomy, physiology, and genetics. We assessed the suitability of an in vitro air-liquid interface (ALI) culture system for newborn pig trachea (NPTr) cells as a practical tool for analyzing the immune response of respiratory epithelial cells to aggressors. This cell line offers a wide microbial susceptibility spectrum to both viruses and bacteria. The purpose of our study was to evaluate and characterize diverse aspects of cell differentiation using different culture media. After the NPTr cells reached confluence, the apical medium was removed and the cells were fed by medium from the basal side. Results We assessed the cellular layer’s capacity to polarize and differentiate in ALI conditions. Using immunofluorescence and electronic microscopy we evaluated the presence of goblet and ciliated cells, the epithelial junction organization, and the transepithelial electrical resistance. We found that the cellular layer develops a variable density of mucus producing cells and acquires a transepithelial resistance. We also identified increased development of cellular junctions over the culture period. Finally, we observed variable expression of transcripts associated to proteins such as keratin 8, mucins (MUC1, MUC2, and MUC4), occludin, and villin 1. Conclusions The culture of NPTr cells in ALI conditions allows a partial in vitro representation of porcine upper airway tissue that could be used to investigate some aspects of host/respiratory pathogen interactions.