Stability is a well-known challenge for rotating systems supported by hydrodynamic bearings (HDBs), particularly for the condition where the misalignment effect and the parametric uncertainty are considered. This study investigates the impact of misalignment and inherent uncertainties in bearings on the stability of a rotor-bearing system. The misalignment effect is approximately described by introducing two misaligned angles. The characteristics of an HDB, such as pressure distribution and dynamic coefficients, are calculated by the finite difference method (FDM). The stability threshold is evaluated as the intersection of run-up curve and borderline. Viscosity and clearance are considered as uncertain parameters. The generalized polynomial chaos (gPC) expansion is adopted to quantify the uncertainty in parameters by evaluating unknown coefficients. The unknown gPC coefficients are obtained by using the collocation method. The results obtained by the gPC expansion are compared with those of the Monte Carlo (MC) simulation. The results show that the characteristics of the HDB and the stability threshold are affected by misalignment and parameter uncertainties. As the uncertainty analysis using the gPC expansion is performed on a relatively small number of predefined collocation points compared with the large number of MC samples, the method is very efficient in terms of computation time.