During the last decade molecular diagnostic techniques have moved from the research laboratory into the clinical microbiology laboratory. The application of molecular biology for the diagnosis of infections and parasitic diseases by the detection of nucleic acids has steadily grown, and it is very probably that, while they may not displace the traditional diagnostic laboratory, they will be common place in the not to distant future. A detailed description of the principal molecular diagnostic techniques that are currently being used or that have a potential use for the diagnosis, evaluation of disease progression or response to therapy of selected infectious and parasitic diseases, is presented. Emphasis is placed on the rational use of these techniques in regional reference laboratories or highly specialized hospitals; the importance of selecting and implanting those diagnostic techniques with the highest cost-benefit ratio; and finally, the need to train human resources which are highly qualified in the theory and practice of molecular biology.