PCR offers a rapid, sensitive and highly specific method for detection of Mycobacterium tuberculosis mainly in sputum but also in other bodily fluids. Identification of Mycobacterium species by acid fast staining requires a highly trained microbiologist/microscopist and can often be midiagnosed because acid fast bacilli are very thin and may be present at very low counts in clinical samples. Identification of Mycobacteria by microbiological growth is both cumbersome and time consuming as many of the pathogenic Mycobacteria species are slow growers. Using PCR as a powerful tool for diagnosing Mycobacterial infection allows the clinicians to make early informed decisions about the proper handling of patients infected with Mycobacteria. This has become more critical with the emergence of multiple drug resistant Mycobacterium species.