The identification of pathogens is of vital importance for the adequate treatment of infections. Compared to classic detection procedures, molecular biology methods allow for swifter identification of pathogens with high sensitivity and specificity. In dermatopathology, PCR-based procedures are employed for the detection of bacteria (Borrelia, Treponema pallidum , mycobacteria), viruses (among others herpesviruses, Merkel cell polyomavirus), fungi (dermatophytes, molds), and parasites (e.g., Leishmania). When interpreting molecular biology findings, the peculiarities of each pathogen have to be taken into account. This especially includes their epidemiology, the type of infection (replicative-productive vs. latent), their cellular reservoirs, and the expected number of pathogens dependent on disease duration. Correlating these findings with clinical and histologic results is pivotal. The present review discusses the significance of molecular biology in the diagnosis of infectious skin diseases. It describes the indications, sensitivity, and limitations of such methods for the detection of pathogens in skin specimens compared to other detection techniques. © 2013 The Authors.