Diesel engines are widely used in the transportation and power generation sectors because of their high fuel efficiency. However, they are responsible for a significant portion of atmospheric oxides of nitrogen and particulate matter, and most run on petroleum derived No. 2 diesel fuel, which is steadily increasing in price. Biodiesel is a notable alternative to diesel fuel because it comes from natural sources, it is essentially carbon dioxide neutral, and it lowers an engine's emission of most pollutants as compared to No. 2 diesel. However, the use of biodiesel often slightly increases a diesel engine's emission of nitrogen oxides (NOx). 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 a new theory explaining this NOx increase; the increase in double bonds in biodiesel, compared to No. 2 diesel, increases its flame temperature, which in turn increases NOx. Numerical simulations found that NOx was predominantly due to the Zeldovich mechanism.