Rotating machinery is the heart of many industrial operations, but many engineers and technicians perform shaft alignment by guesswork or with limited knowledge of the tools and methods available to accurately and effectively align their machinery shaft alignment has increased dramatically. It would therefore appear that shaft alignment seems to have taken a more important role when installing and maintaining machinery Effects of shaft misalignment is reduction in operating life span of rotating machinery since the components that are most likely to fail are the bearings, seals, coupling, and shafts due to inaccurately aligned machinery. In fact, quality alignment is not dependent on the type of measurement system used. Any good dial indicator set is sufficient to perform quality alignments. In this paper the effects of shaft misalignments on the natural frequency of the shaft will be investigated numerically.