Several regulatory challenges are encountered when proceeding towards human clinical trials with gene therapy products, one of these relating to the validity of the analytical methods. Many of the analytical methods used in preclinical studies and/or for analysing the gene therapy products are not yet recognized as a standardized pharmacopoeial methods. Thus, their validity should be demonstrated for the regulatory authorities by thorough assay validations, the extent being dependent on the product developmental stage. We hereby provide an overview on the critical parameters that have to be taken into consideration during the optimization and validation of bio-analytical methods such as PCR, enzyme-linked immunospot assay, Microarray and Limulus Amebocyte Lysate analyses.