The present invention arises from a formulation study in order to define the best excipients including buffer, surfactant, sugar and amino acid to stabilize Flagellin during mesh-nebulization. One of the key factors in stabilising proteins is determining the optimal pH and buffer system to provide adequate solubility and stability and avoid aggregate formation during the aerosolization process. Different formulation have been assayed in order to obtain a stable and soluble aerosol composition comprising flagellin polypeptide in particular considering the choice of the buffering agent, the surfactant and the pH of the liquid formulation comprising the flagellin polypeptide in order to maintain the activity of the flagellin after the aerosolization process. Accordingly, the present invention relates to an aerosol composition comprising droplets comprising a liquid formulation, wherein the liquid formulation, comprises a flagellin polypeptide, a buffer (acetate and/or phosphate) and a surfactant (polysorbate).The aerosol composition of the present invention is suitable for the treatment of lung bacterial infections.