Control of retrotransposon expression in the mammalian germline is regulated by Argonaute family PIWI proteins and their associated small non-coding RNAs known as PIWI-interacting RNAs (piRNAs). To date, no study has demonstrated clear PIWI protein expression nor identified a cellular function(s) for PIWI proteins in the mammalian soma. In contrast to the germline-restricted expression of piRNA associated proteins, we observed that Miwi2 mRNA was induced specifically in epithelial cells during pneumococcal pneumonia. Further investigation showed that similar to its mRNA, MIWI2 protein was indeed expressed outside of the mammalian germline, and was localized to the cytoplasm of a discrete population of multiciliated lung epithelial cells. Immunoprecipitation of MIWI2 from whole lung lysates indicated that it was bound to a small RNA that was longer than a traditional piRNA. Microarray analysis revealed that depletion of MIWI2 in a murine epithelial cell line or in a whole animal model had no effect on retrotransposon expression, further suggesting that lung MIWI2 is independent of nuclear piRNA silencing pathways. Under basal conditions, MIWI2 was required for the normal maintenance of airway epithelial cell fate. In fact, Miwi2 deficiency resulted in an increase in club cells and decrease in ciliated cells indicating that MIWI2 could play a primary role in mucociliary homeostasis or clearance. Similarly, as MIWI2 is induced during lung infection we sought to determine if it participated in host innate immune responses to bacterial infection. Using a clinically relevant model of community acquired pneumonia, Miwi2 deficient mice exhibited an increased expression of inflammatory mediators and immune cell recruitment thus leading to enhanced bacterial clearance. Taken together, these data support the notion that MIWI2 exerts piRNA-independent functions outside of the germline in the ciliated lung epithelium to regulate innate immunity during pneumonia. More broadly, these studies shed light on new areas in PIWI protein and lung ciliated cell biology, and may have implications for multiple diseases including cancer, inflammatory disorders, and infectious diseases.