That is a great question.  A totally 100% answer may never be given - as long term effects we may never know.  But we do know that Biodiesel is the only alternative fuel to have fully completed the health effects testing requirements of the Clean Air Act.  Biodiesel burned in a conventional diesel engine will have a substantial reduction of unburned hydrocarbons, carbon monoxide and particulate matter compared to regular diesel fuel.

Also the exhaust emissions of the sulfur oxides and sulfates from biodiesel are essentially eliminated compared to regular diesel fuel.

Based on engine testing, using the most stringent emissions testing protocols required by EPA for certification of fuels or fuel additives in the US, the overall ozone forming potential of the speciated hydrocarbon emissions from biodiesel was nearly 50% less than that measured for diesel fuel.