Macroscopic studies and scanning electron microscope (SEM), as well as transmission electron microscope (TEM) research were carried out to investigate the nature and properties of particulate matter (PM) deposited in three diesel particulate filters (DPFs) operating with different fuels: 100% rapeseed methyl ester (RME100), a blend of 20% RME and 80% diesel (RME20), as well as 100% diesel (RME0). The DPFs were catalytically coated with V₂O₅/TiO₂. The PM deposits were either extracted from sectioned DPFs or studied "in situ," as deposited. In the RME100-DPF, the lowest soot and highest ash depositions are found. The higher amount of ash in RME100-DPF, as well as the higher participation of the element Ca in the ash from this filter, indicates that in addition to lubricating oil, the RME fuel contributes also to ash formation. Ash is found accumulating in the plugged inlet channels only in RME100 and as a few tens of μm-thick layer on the channel walls of all three filters. Most commonly, ash is mixed with fibers deriving from the gasket on the DPF inlet surface, fibers from the intumescing mat around the DPF and the diesel oxidation catalyst (DOC) upstream the DPF, as well as with newly formed V-O long-prismatic nanocrystals originating from the catalytic coating layer. SEM images reveal the presence of a 130-170 μm thick soot cake on the filter walls of RME20- and RME0-DPF. In RME100-DPF, the soot cake is thinner (ca. 100 μm) and is not any more attached on the channel walls but rather occurs as fragments within the filter channels. EDX analyses of the layer deposited on the channel walls underneath the soot reveal the following elements: Ca, P, Zn, Mg, S, Na (typical ash elements), V, Ti, W (deriving from the catalytic coating) and Fe, Cu from engine wear. The size distribution of individual soot particles in the soot aggregates (average diameter: 21 nm), together with the nanostructure of soot particles obtained by high resolution transmission electron microscopy (HRTEM) indicate that the RME100 soot is relatively more reactive compared to diesel soot.