<p>This paper aims to study the dynamic behavior of an on-board misaligned rotor supported by ball bearings with squeeze film where the inner ring has waviness. The rotor base is, therefore, subject to vibrations. It is excited by both internal imperfections and its base motion. A dynamic model representing this defective rotor is developed. The model accounts for the harmonic translation of the base which is coupled to the excitation due to the misalignment. A new approach based on the harmonic quadrature method (HQM) is developed to solve the equations of motion. The proposed method is validated using data from the literature. The dynamic response of the system is analyzed using bifurcation diagrams, rotor orbits, and spectral analyses. Results show that in the case of a fixed base, the response is periodic and multi-harmonic when the rotor crosses the different sub-harmonics of the system’s critical speed. This is mainly due to the various frequency components induced by the misalignment. The study also shows that the harmonic vibration of the base affects the response of the misaligned rotor. Therefore, as the amplitude of these vibrations increases, the base motion frequency becomes dominant in the rotor response, which may subsequently compromise the accurate diagnosis of a faulty rotor.</p>