In this study, the oxidation characteristics of biodiesel fuels are investigated with the goal of contributing toward the fundamental understanding of their combustion characteristics and evaluating the effect of using these alternative fuels on engine performance as well as on the environment. The focus of the study is on pure fatty acid methyl-esters (FAME) that can serve as surrogate compounds for real biodiesels. The experiments are conducted in the stagnation-flow configuration, which allows for the systematic evaluation of fundamental combustion and emission characteristics. In this paper, the focus is primarily on the pollutant emission characteristics of two C-4 FAMEs, namely, methyl-butanoate and methyl-crotonate, whose behavior is compared with that of n-butane and n-pentane. To provide insight into the mechanisms of pollutant formation for these fuels, the experimental data are compared with computed results using a model with consistent C-1-C-4 oxidation and NOx formation kinetics.