Biodiesel is a transparent amber-yellow liquid with a viscosity similar to petrodiesel, the industry term for diesel produced from petroleum. It can be used as an additive in formulations of diesel to increase the lubricity of pure ultra-low sulfur petrodiesel (ULSD) fuel. Much of the world uses a system known as the "B" factor to state the amount of biodiesel in any fuel mix, in contrast to the "BA" system used for bioalcohol mixes. For example, fuel containing 20 % biodiesel is labeled B20. Pure biodiesel is referred to as B100.

The common international standard for biodiesel is EN 14214.

There are additional national specifications. The standard ASTM D 6751, which is the most common standard referenced in the United States. In Germany, the requirements for biodiesels are fixed in the DIN EN 14214 standard. There are standards for three different varieties of biodiesel, which are made of different oils:

• RME (rapeseed methyl ester, according to DIN E 51606)
• PME (vegetable methyl ester, purely vegetable products, according to DIN E 51606)
• FME (fat methyl ester, vegetable and animal products, according to DIN V 51606)

The standards ensure that the following important factors in the fuel production process are satisfied:

• Complete reaction.
• Removal of glycerin.
• Removal of catalyst.
• Removal of alcohol.
• Absence of free fatty acids.

Basic industrial tests to determine whether the products conform to the standards typically include gas chromatography, a test that verifies only the more important of the variables above. More complete testings are more expensive. Fuel meeting the quality standards is very non-toxic, with a toxicity rating (LD50) of greater than 50 mL/kg.

Biodiesel can be mixed with petroleum diesel at any concentration in most modern engines, although it has the disadvantage of degrading rubber gaskets and hoses in vehicles manufactured before 1992. Biodiesel is a better solvent than petrodiesel and has been known to break down deposits of residue in the fuel lines of vehicles that have previously been run on petroleum. Fuel filters may become clogged with particulates if a quick transition to pure biodiesel is made, but biodiesel cleans the engine in the process. It is therefore recommended, to change the fuel filter 800 miles after switching to biodiesel. In a study at a U.S. military base[citation needed], a biodiesel blend was used as a replacement for heating oil at housing on the base. Due to the good solvating ability of biodiesel, residues that had been present in fuel tanks for decades were dissolved. The particulate component of the residues caused repeated clogging of fuel strainers, requiring repeated replacement, cleaning, and in some cases installation of higher capacity filters. Due to the relatively smaller surface area and service life of fuel tanks in motor vehicles and mobile equipment, filter clogging is less prevalent but still a factor to be considered.