Vector persistence in blood is commonly examined during the development and use of gene transfer medicine. Reliable and standardised analysis of transgenes in blood also forms the basis of detecting the misuse of gene transfer technology in sport, called gene doping. The current study tested the effect on vector detection of blood samples stored at different temperatures for different time periods. As a model system, we used nonviral and AAV vectors carrying the human erythropoietin transgene spiked at 1500 copies per millilitre of blood from eight donors. Using previously optimised methods for DNA extraction and real-time PCR transgene detection, we followed the developed protocols for sample processing prior to storage and for sample freezing, and showed that storage of blood samples at -80°C for at least six months did not affect the reliability of transgene analysis. Storing samples for 3 months at -80°C or -20°C is equally acceptable, while storage for up to 30 days can be done in a fridge or at -80°C or -20°C without affecting transgene detection. More informative and reliable results from vector clearance studies in gene therapy and consistent inter-laboratory comparisons may be attained by the adoption of these described protocols.