Estimation of measurement uncertainty is important as it provides objective evidence that an assay or instrument is 'fit for purpose', and is a requirement for accreditation to ISO17025. Technological developments within the bioanalytical laboratory have progressed rapidly in the past few years. However, the measurement science associated with these technologies has not yet fully matured. The provision of a full measurement uncertainty budget is often difficult because of a lack of standardised approaches and the constraints associated with time, finances and expertise. A procedural approach for the identification of factors that can account for measurement uncertainty in quantification of genetically modified (GM) ingredients using real-time quantitative PCR is presented here. This example illustrates an approach for the identification of factors that can be applied to related assays concerned with GM quantification, can be utilised as part of existing uncertainty approaches, and can provide the basis for making quantitative estimates of uncertainty that will contribute towards a full measurement uncertainty budget.