Biodiesel fuels, made up primarily of fatty acid methyl esters (FAME), are advantageous because they are renewable and generally have lower pollutant emissions. In order to study in detail the effect of the FAME molecular structure on the combustion chemistry, a saturated (i.e., methyl butanoate) and an unsaturated (i.e., methyl crotonate) C4 FAME were oxidized in an opposed flow diffusion flame and a jet stirred reactor. Some consistent trends were seen in both experiments. Both fuels have similar reactivity. The experimental results show that methyl crotonate combustion produces much higher levels of C2H2, 1-C3H4, 1-C4H8, and 1,3-C4H6 than methyl butanoate. The methyl butanoate combustion had higher levels of C2H4. In the opposed flow diffusion flames, the methyl crotonate also produced benzene while for methyl butanoate it was not detected. These species are relevant to soot formation. In addition, the experiments measured higher levels of 2-propenal, methanol, and acetaldehyde for methyl crotonate than for methyl butanoate. The reactions controlling these differences are discussed.