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GMO detection and quantification methods in the EU are mainly based on real-time PCR. The analytical methods in use must be validated, first on an intra-laboratory scale and through a collaborative trial thereafter. Since a consensual protocol for intra-laboratory validation of real-time PCR methods is lacking, we provide a practical approach for the in-house validation of quantitative real-time PCR methods, establishing acceptability criteria and quality controls for PCR runs. Parameters such as limit of detection, limit of quantification, precision, trueness, linear dynamic range, PCR efficiency, robustness and specificity are considered. The protocol is sufficiently detailed to be directly applicable, increases the reliability of results and their harmonization among different laboratories, and represents a necessary preliminary step before proceeding to a time-consuming and costly full validation study.