In recent years, replacement of conventional microbiological culture-based diagnostic testing with molecular detection of bacterial, fungal and viral pathogens has become routine across many laboratories. This increase in adopting molecular methods has been primarily due to the availability of automated instrumentation that can provide results in a timely and efficient manner, without the need for in-depth knowledge of molecular biology. The use of molecular methods is therefore translating into better treatment, care and management of patients. Advancement in instrumentation has occurred across all stages of molecular testing from pre- to post-analytical stages of testing. This short summary is by no means exhaustive of all systems available or soon to become available; however, it gives a brief overview of the most common instruments in use and also some of the advancements that are in the process of becoming available.