This paper proposes a modified Reynolds equation for the coupled journal and thrust fluid dynamic bearings (FDBs) to include variable film thickness due to imperfect roundness of a rotating shaft. A finite element method is used to solve the modified Reynolds equation to calculate the pressure. Reaction force, moment, and friction torque of FDBs are calculated by integrating the pressure and shear stress along the fluid film. The dynamic behavior of a hard disk drive (HDD) spindle system is investigated by solving the equations of motion with six degrees of freedom using the Runge-Kutta method. This research shows that the imperfect roundness of the shaft increases the nonlinearity of FDBs. Imperfect roundness of the shaft generates harmonics of the groove number plusmn 1 in the bearing reaction force and the displacement of the HDD spindle system even in the case of stationary grooved FDBs.