The diagnostic applications of the molecular biology in infectious diseases are wide and applicable to any diagnostic problem. In the Herpesviridae family, the most used methods are those based on the amplification of DNA polymerase gene for the detection of HSV 1 and 2, varicela-zoster, citomegalovirus, Epstein Barr virus and HHV6 simultaneously. This methodology has been able of detect the co-infection of HSV1 and VZV in samples of CNS fluid. In citomegalovirus, molecular methods are used in the monitoring of the reactivation of CMV in immunosuppressed patients and are able to detect viral reactivation within 1 week before symptoms. The molecular methods are also able to identify the Epstein-Barr virus in a proportion of 8 to 20% of gastric cancer cases harboring a unique strain in spite of the presence multiples strains in the healthy population. These associations between virus and cancer have also been described for the human papilloma virus and esophageal and lung cancer. In bacterial agents, the detection and quantification of Bordetella pertussis is another interesting application since it might become a method for rapid diagnosis and predictive of severity in children less than 6 months old. The identification of Helicobacter pylori strains in relation to gastric cancer and peptic ulcer disease and the characterization of strains of methicillin resistant Staphylococcus aureus are other examples of potential applications of the molecular methods in typing microorganisms. In the diagnosis of respiratory tract infectious agents such as Mycobacterium tuberculosis, Pneumocystis carinii and atypical agents, the molecular methods allow the diagnosis in non-invasive samples. Finally, these new methodologies also contribute to the diagnosis of systemic mycotic agents (Candidiasis and Aspergillosis) particularly in immunosuppressed patients