This paper presents a real successful implementation of lean six sigma methodology to continuously improve the baggage flow in a baggage handling system (BHS), by identifying the causes of mishandled baggage, and deriving solutions to enhance BHS performance. The results show that the main critical problems were low system reliability and the high number of bags passing through manual-encoding-stations. This research illustrates how to avoid baggage congestion and provides applicable and cost-effective solutions. The success of this project made the organisation aware of the opportunities that the application of lean Six Sigma methodology created in the aviation and airport sector.