This document describes the performance characteristics and minimum performance criteria for conducting a single-laboratory validation study for qualitative (binary) real-time polymerase chain reaction (PCR) methods applied for the detection of specific DNA sequences present in foods. The protocol was developed for qualitative real-time PCR methods for the detection of DNA sequences derived from genetically modified foodstuffs. It is applicable also for single-laboratory validation of qualitative PCR methods used for analysis of other food materials, e.g. for species detection and identification. The document does not cover the evaluation of the applicability and the practicability with respect to the specific scope of the PCR method.