Randomised experimental designs are considered statistically advantageous for many scientific applications, as they reduce the effect of problematic parameters such as sample position. The effect of randomisation was assessed using real-time PCR experiments for the determination of genetically modified material. Replicate microtitre plates using a randomised design were compared with replicate microtitre plates that contained the same samples allocated in a systematic fashion to experimental position within the plate. Results indicated that randomisation would help reduce between-plate variability and would give advantages in intra-laboratory studies. However, these benefits may be less effective for inter-laboratory studies as the between-laboratory variability often far exceeds the between-plate variability.