Influence of dissimilar radial clearances of the two end bearings on the performance of hydrodynamic rotor-bearing systems is investigated in the present paper. The rotor misalignment effects are considered. A parameter ξ is introduced to measure the dissimilar level and three typical applied points ( Case Left, Case Center, and Case Right) of external load are also investigated during the analysis. Finite difference method is adopted to solve the Reynolds-type equation and verification of the solution technique is conducted by comparison with previous work. The rotor equilibrium postures are solved at different dissimilar parameters ( ξ) for the three external loading situations. Results show that dissimilar radial clearances have significant effects on rotor postures, minimum film thickness, stiffness and damping coefficients. Under unbalanced load situations ( Case Right, Case Left), small values of ξ (<1.0) will alleviate and large one ξ (>1.0) will aggravate the misaligned effects. Meanwhile, the minimum film thickness increases with ξ (<1.0) and decreases with ξ (>1.0). For stiffness and damping coefficients, the variations with ξ have no obvious rules. During the design and analysis of hydrodynamic rotor-bearing systems, the dissimilarity should be considered intensively for reaching appropriate results.