The remarkable safety of air travel compared to land transport is achieved through systematic risk management, failure investigation, and continuous improvement. A crucial area where these principles are applied is in preventing fuel system issues caused by aviation fuel contamination, which can pose acute and long-term risks during storage, transport, or use in aircraft fuel systems. Fuel quality assurance (QA) laboratories employ standardized protocols to ensure that aviation fuels comply with the specifications and limits defined in standard test methods and to detect many contaminants that can cause considerable short-term damage to the fuel system. However, routine analysis cannot identify numerous other contaminants that might severely damage the ground and aircraft fuel systems. In addition, to prevent re-contamination, the nature and source of the contamination must be determined. Where contamination is suspected, analytical chemistry laboratories have methods for deep fuel analyses that can meet these challenges. This chapter provides a general overview of some contaminants often found in fuels and suggests ways to detect them.