Modern aviation requires reliable and safe sources of fuel which means fuel is frequently stored for extended periods. In addition, as fuel is used, new fuel is added which is not always compatible with the fuel in the tank. The incompatibility and long-term storage leads to a number of problems that will be addressed in this chapter. Some of the possible changes over time include formation of bioilms, deposit formation, water incorporation and additive depletion. The chemistry and biochemistry of each of these areas will be discussed along with how they might be prevented. New areas of research on low temperature oxidation of trace fuel components and the prevention of bacterial growth will be presented. Other problems are related to the reaction of trace components in the fuel which can lead to oxidation and deposit formation. Trace components also vary based on fuel source and lead to problems in compatibility of diferent fuels. In addition some of the reactions of fuel additives will be discussed.