Pure, non-blended biodiesel can be poured straight into the tank of any diesel vehicle. As with normal diesel, low-temperature biodiesel is sold during winter months to prevent viscosity problems. Some older diesel engines still have natural rubber parts which will be affected by biodiesel, but in practice these rubber parts should have been replaced long ago. Biodiesel is used by millions of car owners in Europe (particularly Germany).
Research sponsored by petroleum producers has found petroleum diesel better for car engines than biodiesel. This has been disputed by independent bodies, including for example the Volkswagen environmental awareness division, who note that biodiesel reduces engine wear. Pure biodiesel produced 'at home' is in use by thousands of drivers who have not experienced failure, however, the fact remains that biodiesel has been widely available at gas stations for less than a decade, and will hence carry more risk than older fuels. Biodiesel sold publicly is held to high standards set by national standards bodies.
The temperature at which pure (B100) biodiesel starts to gel varies significantly and depends upon the mix of esters and therefore the feedstock oil used to produce the biodiesel. For example, biodiesel produced from low erucic acid varieties of canola seed (RME) starts to gel at approximately −10 °C (14 °F). Biodiesel produced from tallow tends to gel at around +16 °C (68 °F). As of 2006, there are a very limited number of products that will significantly lower the gel point of straight biodiesel. A number of studies have shown that winter operation is possible with biodiesel blended with other fuel oils including #2 low sulfur diesel fuel and #1 diesel / kerosene. The exact blend depends on the operating environment: successful operations have run using a 65% LS #2, 30% K #1, and 5% bio blend. Other areas have run a 70% Low Sulfur #2, 20% Kerosene #1, and 10% bio blend or an 80% K#1, and 20% biodiesel blend. According to the National Biodiesel Board (NBB), B20 (20% biodiesel, 80% petrodiesel) does not need any treatment in addition to what is already taken with petrodiesel.
Some people modify their vehicles to permit the use of biodiesel without mixing and without the possibility of gelling at low temperatures. This practice is similar to the one used for running straight vegetable oil. They install a second fuel tank (some models of trucks have two tanks already). This second fuel tank is insulated and a heating coil using engine coolant is run through the tank. There is then a temperature sensor installed to notify the driver when the fuel is warm enough to burn, the driver then switches which tank the engine is drawing from.
Biodiesel may contain small but problematic quantities of water. Although it is hydrophobic (non-miscible with water molecules), it is said to be, at the same time, hygroscopic to the point of attracting water molecules from atmospheric moisture; in addition, there may be water that is residual to processing or resulting from storage tank condensation. The presence of water is a problem because:
- Water reduces the heat of combustion of the bulk fuel. This means more smoke, harder starting, less power.
- Water causes corrosion of vital fuel system components: fuel pumps, injector pumps, fuel lines, etc.
- Water freezes to form ice crystals near 0 °C (32 °F). These crystals provide sites for nucleation and accelerate the gelling of the residual fuel.
- Water accelerates the growth of microbe colonies, which can plug up a fuel system. Biodiesel users who have heated fuel tanks therefore face a year-round microbe problem.
Biodiesel can also be used as a heating fuel in domestic and commercial boilers. A technical research paper published in the UK by the Institute of Plumbing and Heating Engineering entitled "Biodiesel Heating Oil: Sustainable Heating for the future" by Andrew J. Robertson describes laboratory research and field trials project using pure biodiesel and biodiesel blends as a heating fuel in oil fired boilers. During the Biodiesel Expo 2006 in the UK, Andrew J. Robertson presented his biodiesel heating oil research from his technical paper and suggested that B20 biodiesel could reduce UK household CO2 emissions by 1.5 million tonnes per year and would only require around 330,000 hectares of arable land for the required biodiesel for the UK heating oil sector. The paper also suggests that existing oil boilers can easily and cheaply be converted to biodiesel if B20 biodiesel is used.