The manufacturing tolerances of a hydrodynamic journal bearing system are inevitable in manufacturing process. To examine and understand the effect of manufacturing tolerances on the system stability can help engineers to confidently choose reasonable tolerances at design stage. This study presented a theoretical analysis method to determine and compare the effects of dimensional manufacturing tolerances and journal out-of-roundness on system stability by Taguchi method. The results show that the journal out-of-roundness has the most significant effect on the system stability and the journal out-of-roundness appears to stabilize the system. The authors suggest that both dimensional manufacturing tolerances and journal roundness should be taken into account in the design of cylindrical journal bearings.