A particular kind of biofuel is similarly earmarked for the jet fuel market, and this fuel is built to withstand the unique pressure of performing at high altitude and in extreme temperatures. Even as airlines test this fuel, they are quite terrified that some of the other stuff will wind up in their tanks.
This concern isn't misplaced. The close relationship between diesel and jet fuel mean that the traditional fuels tend to be shipped in the same tanks, trains and pipelines, co-mingling on the edges. As biodiesel starts to make its way into traditional diesel, the fear is that biodiesel will start to show up in ever greater concentrations in jet fuel. And while biodiesel might work in your truck or school bus most of the time, you wouldn't want to rely on the stuff at 35,000 feet in the air.
Engine-makers like Rolls Royce, Pratt & Whitney, and Westinghouse generally give pretty strict guidance on how much biodiesel can show up in jet fuel before they can no longer guarantee the performance of their engines. Right now that limit can be as high as 30 parts per million, or as low as 5 ppm. Shared transport of diesel and jet fuel could easily push trace biodiesel in jet fuel much higher that those kinds of limits.
Jet engine makers give biofuels a pretty chilly reception. In a typical review of how airlines can better engage with the environment, Pratt & Whitney recently pushed alternative solutions like keeping engines cleaner, and cutting fuel burn with more advanced engines. Of course, it helps that these solutions would help sell more engines. But the report also points out that the debate rages on about whether using crops for transport fuel of any kind hurts the world more than it helps it.
For its part, IATA's fuel working group seems to be trying to take some of the hysteria out of the debate by adopting guidance that jet engines will work normally with up to 100ppm of biodiesel in the jet fuel tank, and currently hopes to have that guidance stamped by the end of the year. Previous deadlines have passed, though, and with such strong feeling in the air, I wouldn't be surprised if it slips again.