In a geological repository, the production of gas is unavoidable. Dissolved gas is transported away from the repository by diffusion as dissolved species. If the rate of gas generation is larger than the diffusive flux into Boom Clay, the pore water within the disposal gallery will become oversaturated and a free gas phase might form. In order to make a good evaluation of the balance between gas generation and gas dissipation, good estimates for the gas diffusion coefficients of the gases are needed. The currently available gas diffusion parameters for hydrogen in Boom Clay suffer from a large uncertainty, and by application of conservative values for both the source term and the gas migration term the formation of a free gas phase can presently not be excluded for some waste types. In this study a versatile method was developed to determine more precisely the gas diffusion coefficient for dissolved gases in Boom Clay. The proposed method is based on a through diffusion methodology. The apparent diffusion coefficients of dissolved He and CH4 were obtained: 12.2 × 10−10 and 2.42 × 10−10 m2/s, with uncertainties of 10%, respectively.