The recent developments in diesel fuel injection equipment coupled with the moves in the US to using ULSD and biodiesel blends has seen an increase in the number of reports from both engine manufacturers and fleet operators regarding fuel system deposit formation issues. These deposits not only form on and within the fuel injectors but they also form elsewhere in the fuel system, due to fuel recirculation. These will eventually accumulate in the fuel filters. Historically, diesel fuel system deposits have been attributed to contamination of the fuel or the degradation of the fuel with age. Such age related degradation has been attributed to oxidation of the fuel via well documented pathways, although the initiation of this process is still poorly understood. Papers at recent SAE meetings in Florence, San Antonio, Rio de Janeiro, San Diego and Kyoto have addressed many of these causes.However, in recent cases the deposits internal to the fuel injector have become prevalent and characterisation of the deposits on the injector needle has become an industry priority. The deposits are different from those traditionally encountered, with inorganic and carbon components being found. This paper will describe for the first time the application of Time-of-Flight Secondary Ion Mass spectrometry (ToF-SIMS), for the analysis of these deposits. This technique involves: surface spectroscopy; static SIMS, the application of very low primary ion dose densities yielding quasi nondestructive surface analysis. Combined with surface imaging which involves the rastering of a finely focussed ion beam over the surface yielding mass resolved secondary ion images; chemical maps, and depth profiling. Every pixel of a ToF-SIMS map represents a full mass spectrum. The technique also allows dynamic SIMS; and 3D Rendering. Where the application of high primary ion dose densities to the sample yields, successive removal of top surface layers and from the resultant mass spectra elemental in-depth distribution. Thus for the first time both the surface and the inner layers of a deposit may be characterised in three dimensions.This paper also discusses the insights that such analysis can bring to the constitution, origin, and build-up history of these deposits and could provide a basis for the development of strategies to minimise such deposit formation.