Biodiesel contains a variety of compounds, depending on the production and the provenance of the fuel. During the production process and usage, some of these compounds can form deposits (nozzle tip deposits or internal diesel injector deposits: “IDID”), which may lead to severe problems, such as corrosion, filter blockage and other technical issues. To deal with these difficulties, it is essential to exactly determine the components of these deposits. Most analytical methods used before, require complex preparations and result in limited information of the deposit material. Using infrared microscopy (ATR-FTIR: Attenuated-Total-Reflection Fourier-Transform-Infrared-Spectroscopy) or mass spectrometry (TOF-SIMS: Time-of-Flight Secondary-Ion-Mass-Spectrometry), a direct analysis of the original deposit material is possible.In order to analyze the chemical composition of the deposits, samples were taken from affected engine parts and filling stations and examined with a TOF-SIMS instrument and a common infrared microscope. Infrared investigations of the engine parts hint to the presence of carboxylic acid salts and mass spectra of the same samples indicate various organic compounds, partly based on polyisobutylene succinimides (“PIBSI”). In the spectra of plugged fuel filters peak-pattern of different sterol glucosides and related compounds are observed. The analyses of directly taken biodiesel samples reveal ingredients such as fatty acid methyl esters (FAME) and steryl esters among other things, so that very detailed descriptions of the fuel constitution are possible. Altogether these investigations show that the combination of infrared spectroscopy and TOF-SIMS is a powerful tool, which provides a large amount of information in order to gain a detailed insight in the formation of these deposits.