Majority of modern diesel engines is fitted with common-rail (CR) fuel systems. In these systems, the injectors are supplied with fuel under high pressure from the fuel rail (accumulator). Dynamic changes of pressure in the fuel rail are caused by the phenomena occurring during the fuel injection into the cylinders and the fuel supply to the fuel rail through the high-pressure fuel pump. Any change in this process results in a change in the course of pressure in the fuel rail, which, upon mathematical processing of the fuel pressure signal, allows identification of the malfunction of the pump and the injectors. The paper presents a methodology of diagnosing of CR fuel injection system components based on the analysis of dynamic pressure changes in the fuel rail. In the performed investigations, the authors utilized LabView software and a µDAC data acquisition module recording the fuel pressure in the rail, the fuel injector control current and the signal from the camshaft position sensor. For the analysis of the obtained results, ‘FFT’ and ‘STFT’ were developed in order to detect inoperative injectors based on the curves of pressure in the fuel rail. The performed validation tests have confirmed the possibility of identification of malfunctions in the CR system based on the pressure curves in the fuel rail. The ‘FFT’ method provides more information related to the system itself and accurately shows the structure of the signal, while the ’STFT’ method presents the signal in such a way as to clearly identify the occurrence of the fuel injection. The advantage of the above methods is the accessibility to diagnostic parameters and their non-invasive nature.