Molecular testing is increasingly used to supplement or replace conventional microscopy-based methods of parasite identification. Potential benefits of molecular methods such as nucleic acid amplification tests include increased sensitivity, ability to differentiate morphologically similar organisms and lack of reliance on subjective microscopic features. However, several challenges exist for widespread implementation of molecular diagnostics, including the expense of reagents and equipment, need for sophisticated facilities and lack of commercial testing options. Most molecular parasitology tests are based on non-standardised laboratory-developed methods, although new commercial options including multiplex methods for gastrointestinal pathogens have recently become available. This review will focus on the use of molecular assays for common and important parasites including Plasmodium and Babesia species, trypanosomes, filaria, Leishmania species, free-living amoebae, Trichomonas vaginalis, Toxoplasma gondii and intestinal protozoa and helminths and how testing can be integrated into patient care algorithms.