Biodiesel is a notable alternative to petroleum derived diesel fuel because it comes from natural domestic sources and thus reduces dependence on diminishing petroleum fuel from foreign sources, it likely lowers lifecycle greenhouse gas emissions, and it lowers an engine’s emission of most pollutants as compared to petroleum derived diesel. However, the use of biodiesel often slightly increases a diesel engine’s emission of smog forming nitrogen oxides (NOx) relative to petroleum diesel. In this paper, previously proposed theories for this slight NOx increase are reviewed, including theories based on biodiesel’s cetane number, which leads to differing amounts of charge preheating, and theories based on the fuel’s bulk modulus, which affects injection timing. This paper proposes an additional theory for the slight NOx increase of biodiesel. Biodiesel typically contains more double bonded molecules than petroleum derived diesel. These double bonded molecules have a slightly higher adiabatic flame temperature, which leads to the increase in NOx production for biodiesel. Our theory was verified using numerical simulations to show a NOx increase, due to the double bonded molecules, that is consistent with observation. Further, the details of these numerical simulations show that NOx is predominantly due to the Zeldovich mechanism.