Sustainable fuels can help to decrease carbon dioxide emissions in road transportation compared to standard fossil fuels. The most common sustainable fuels used today in heavy-duty applications are biodiesel and hydrogenated vegetable oil (HVO). Biodiesel and HVO are known as drop-in fuels since they are fuels that can be blended with standard diesel. However, due to changes in the chemical properties when the fuels are mixed, solubility problems in terms of precipitates may be formed. These insolubilities can lead to deposits in the fuel system, e.g., blocked fuel filters and internal injector deposits, and thus driveability problems. This study is a part of a project where the goal is to study the processes that cause the formation of deposits inside the injectors in heavy-duty vehicles. The deposits inside the injectors are known as internal diesel injector deposits (IDID). To study the formation of IDID, a number of injectors from heavy duty vehicles were collected from two different European markets: one market that uses biodiesel fuel and another that uses HVO as a drop-in fuel. A technique not previously used to identify IDID, namely pyrolysis GC-MS, proved successful in this regard, and FTIR and SEM-EDX methods were also used to characterise the deposits. The results showed that the composition of the IDID´ s from different markets differed. Metal soaps, inorganic salts and nitrogen compounds were found in the deposits taken from the injectors in the biodiesel drop-in market. The source of these components is believed to be degradation and contamination of the biodiesel. In addition, fuel additives such as corrosion inhibitors and detergents were found in the injectors from the market using HVO as a drop-in fuel. This could imply that the poor solvency of HVO can give problems in some additive combinations.