Tolerance stack up is one of the most important exercises of design team to ensure the interchangeability of the components and the sub assemblies in the product having a large product family. Optimized allocation of tolerances between the components in a product helps to reduce the conflicts between the designer and the manufacturer.Automotive gearbox is one of the most important and critical aggregate of any vehicle in which the assembly of gear train performs the function as required. In the gear train, numbers of gears are meshed with each other and transfer the torque on wheels as per the required performance of the vehicle. When the gears are meshed and rotates some noise would generate because of the rolling and sliding action of the gears. This noise is known as “whine noise”. Now days this whine noise is increasingly becoming an important subject for the transmission designers. Gear whine is a total noise that is noticeable to passengers and makes them uncomfortable. Whine noise can be controlled to some extent by optimize the gear micro geometry to reduce the transmission error TE.But only optimization of the gear micro geometry is not sufficient to reduce the transmission error and whine noise. Proper position and assembly of gears in the gear train assembly is also important to improve the gear micro geometry and whine noise. Radial and angular clearances between the two meshed gears, contributes a significant role in increasing the efficiency and performance of gears in terms of noise, vibration and harshness. In this paper we have taken 6 speed manual transmission and shows how the gear radial and tilt stack up analysis helps to reduces the transmission error and increase the efficiency and performance of gear pair in terms of strength, noise, vibration and harshness.