Originally Posted by Shortsguy1

Army-
When you use biodiesel (versus petro-diesel), emissions of particles typically drops and emissions of oxides of nitrogen (NOx) typically goes up. PM is a bigger direct health concern to those near diesels, whereas NOx contributes to the formation of ozone and acid rain. Net CO2 emissions are lower because the plants sucked the CO2 in which is emitted as you drive. But biodiesel is not climate neutral. It takes a lot of energy to grow the plants and process the fuel. So there are CO2 reductions with biodiesel compared to petrodiesel, but it is far from perfect.

There is tons of research (much of it in the SAE journals) on emissions of alternatives fuels. I don't have it in front of me, but I am happy to help people track down emissions data for a particular fuel if interested.