Manufacturers of diesel engines make it clear that small amounts of biodiesel are usually fine (most say B5, or diesel with five percent biodiesel mixed in, is OK), but they won't make any promises about higher concentrations. Popular Mechanics has a good article that explains that these companies aren't just trying to make life difficult for plant-fuel lovers: there's technology in new diesel cars that doesn't play nice with biodiesel. The Environment Protection Agency and the California Air Resources Board implemented new rules that required automakers to design cleaner diesel engines which resulted in diesel particulate filters (DPFs) being installed in new diesel cars. This is a good idea when you're burning petrol diesel - NOx and particulates are captured by the filters - but when you're using biodiesel, those same DPFs are a problem instead of a solution. The short version is that biodiesel's longer hydrocarbon chain means it doesn't act like petrodiesel in the fuel line, and dilutes the engine oil. Popular Mechanics has all the details and it's well worth reading.
[Source: Popular Mechanics]