The detection of molecules of pathogens (antigens and genetic material) and host molecules in response to infections (antibodies) is the basic principle involved in molecular diagnostic tests. These tests have avoided the need to detect the attacking pathogen. New advances in molecular biology and the development of robotic technology and genomic and protein sequencing have allowed for the development of new high performance and highly specific tests. Genomics and proteomics contribute to the identification of biomarkers and biotechnology provides methods to produce high purity reagents. The identification of coding genes of specific antigens, their cloning and recombinant production, the production of monoclonal antibodies, their fragments and single chain antibodies enabled new, safer, high sensitivity and specificity immunological techniques to develop. New recognition molecules, including aptamers, will soon replace the need to produce antibodies by immunization. For the detection of genetic material, new methodological strategies based on hybridization and amplification (PCR, end point and real time) in multiplex and microarray formats have been developed, and for their detection new reporter molecules have been designed that enable their quantification. Although these methods require sophisticated instrumentation, they will soon be accessible for application in public health.