Abstract This work was carried out to identify sources of errors, uncertainties and discrepancies in studies of fuel retention in wall components from the JET tokamak using methods based on thermal desorption. Parallel aims were to establish good practices in measurements and to unify procedures in data handling. A comprehensive program designed for deuterium quantification comprised the definition and preparation of two types of materials (samples of JET limiter Be tiles and deuterium-containing targets produced in the laboratory by magnetron-assisted deposition), their pre-characterization, quantitative analyses of the desorption products in three different thermal desorption spectroscopy systems and a detailed critical comparison of the results. Tritium levels were also determined by several techniques in samples from JET and in tritiated targets manufactured specifically for this research program. Facilities available for studies of Be- and tritium-contaminated materials from JET are presented. Apparatus development, future research options and challenges are discussed.