An enormous amount of data is generated and compiled in several databases every year. Along with this, comes a demand for the analysis and interpretation of the entirety of this biological information. Taking care of this task, bioinformatics promises breakthroughs in research and development in complex biomedical areas. In just a few years since its beginning, bioinformatics has led to great progress and demonstrated its potential. It has created an opportunity to solve arising medical and molecular issues faster and more efficiently, as compared to the traditional approach. The present review aims to present some of the main applications of bioinformatics in the field of biomedicine, such as comparative genomics, biomarker identification, computer-aided drug design, vaccine design, and personalized medicine. In addition, we also cover some of its steadily reduced limitations.