Gear stress analysis and understanding the effect of misalignment and microgeometry is important for gear designers and for those who work in gear maintenance. The misalignment can lead to the higher stress acting in one side of the gear tooth and the micro-geometry modification can improve the stress distribution in the gear teeth. In this research, a helical gear pair was modeled using three different software and tools; LDP, KISSsoft and Abaqus. Three different cases were modeled to study the effect of misalignment and microgeometry. Finally, the results from different tools were presented and discussed. It was observed that the tooth contact analysis software resulted in significantly higher stresses than the FE software. The results have been discussed to understand the differences in the cases obtained from the used tools. The results showed how bad is the effect of the misalignment on the gear mesh and the stress distribution and how the microgeometry modifications are used to compensate that effect.