A challenging task that is required to modern injection systems is represented by the enhanced control of the injected quantities, especially when small injections are considered, such as, pilot and main shots in the context of multiple injections.The propagation of the pressure waves triggered by the nozzle opening and closure events through the high-pressure hydraulic circuit can influence and alter the performance of the injection apparatus. For this reason, an investigation of the injection system fluid dynamics in the frequency domain has been proposed. A complete lumped parameter model of the high-pressure hydraulic circuit has been applied to perform a modal analysis. The visualization of the main vibration modes of the apparatus allows a detailed and deep comprehension of the system dynamics. Furthermore, the possible resonances, which are induced by the action of the external forcing terms, have been identified. These forcing terms are the pump delivered flow-rate, the leakages through the injector pilot-valve, the injected flow-rate and the pressure control valve operation.On the basis of the developed methodology, it is possible to design injection systems with an optimized dynamic response. The sensitivity of the modes of vibration to a relevant geometrical parameter of the injection system has been analyzed and discussed in order to illustrate the practical application of the proposed approach.