In recent years quantitative PCR (qPCR) detection methods have been widely utilised to detect phytopathogenic fungi and oomycetes and have greatly contributed to the advancement of knowledge in plant pathology. However, major drawbacks and common errors, most typical of earlier reports, still affect many methods currently available in the literature. Errors can be made throughout the entire process for the development of qPCR methods, at the level of selection of appropriate DNA extraction and purification protocols, identification of suitable target regions, choice of the chemistry, design and validation of specific primers and probes, analysis of sensitivity, choice of an absolute and/or relative quantification approach and analysis of the risk of detecting target DNA from dead sources. In the present review the above mentioned steps are analysed, highlighting their critical aspects and providing a practical guide for the users.