Yes! Biodiesel is cleaner. A great study that shows the benefits of biodiesel as well as the drawbacks, Biodiesel Handling and Use Guidelines, was done by the National Renewable Energy Laboratory (NREL).

Emissions:
Using biodiesel as fuel in a standard 4 stroke diesel engine leads to reduced emissions. A draft report by the U.S. Environmental Protection Agency (EPA), A Comprehensive Analysis of Biodiesel Impacts on Exhaust Emissions, shows significant reductions in most harmful emissions. This graph, Figure ES-A, shows the findings. Emissions Graph

    The abbreviations are:

  • NOx (sounds like socks) - Nitrogen Oxides, which contribute to ground level ozone, smog, and acid rain.
  • PM - Particulate Matter, is pointed to as a source for respiratory problems and many premature deaths every year.
  • CO - The EPA states that Carbon Monoxide inhibits the bloods ability to carry oxygen to organs and tissues.
  • HC - Hydrocarbons, many with known toxicity, are found naturally in fossil fuels are not present in biodiesel.