The stability of Diesel/Biodiesel blends can play an important role in deposits formation inside the fuel injection system (FIS). The impact of the stability of FAME/Diesel fuel blends on lacquer deposits formation and on the behavior and reliability of the FIS was investigated using blends of Rapeseed and Soybean methyl esters (RME, SME) and conventional Diesel fuel (volume fractions of RME and SME range from 0 to 20%v/v). Fuels were aged under accelerated conditions and tested on an injection test rig according to an operating cycle developed to provoke injector needle blocking. The soaking duration was found to affect injector fouling. A relationship between the injector fouling tendency and the fuel stability was established. Under current test condition, injectors fouling increased with fuel oxidation measured with Total-Acid-Number. Needle fouling occurred at a TAN level of 0.25mg KOH/g and needle blocking occurred at a TAN level of 0.5 and 1 mg KOH/g for B20-SME and B20-RME, respectively. The FAME composition and the fuel ageing procedure can have a significant impact on FIS fouling tendency.