This paper presents several geometrical tolerance (GT) applications and vibration effects in rotational shaft. The impact of vibrations can damage critical components of machines such as bearings, gears and couplings and can be considered as benchmark for fundamental study to reduce the problem and improve the reliability of the components. Variations of GT in shaft models were applied to evaluate geometrical characteristics in translational and rotational parts featuring defects due to position and concentricity errors. The improvement of the shaft performance was conducted using finite element (FE) to establish minimum circumscribed, maximum inscribed and minimum zone. This approach is more accurate to the real model and assembly of mechanical system. The FE was compared with experimental results. Unconstrained vectors are used instead of the vibration frequency analysis to overcome the effects of the assumptions. Vibration frequencies were simulated by Finite Element Analysis of mechanical rotating shaft. It is found that concentricity characteristic has the highest magnitude compared to other characteristic. These effects should be taken into account in the design, installation and maintenance of rotating shafts. The impact and level of damage of the critical parts in the machine can be a benchmark for further studies for tolerance analysis and reliability.