This chapter discusses the chemical kinetics of practical hydrocarbon and biodiesel fuels used in engines. Elementary reactions that provide chain branching are identified, and their role in producing autoignition is explained. Roles of differences in fuel molecular structure, particularly primary, secondary, and tertiary C–H bonds, on rates of combustion and ignition are explained and used to explain how fuel parameters such as octane and cetane numbers depend on the fuel molecule size and structure. Chemical kinetic factors are used to explain the way in which selected additives can improve either the cetane or octane ratings for fuels, through their roles in influencing chain‐branching rates. Examples are provided to illustrate the principles, including very recent studies in biodiesel fuel kinetic modeling.