The distribution of SO3H-functional groups attached to the ordered inner pore walls of mesoporous Si-MCM-41 materials based on SiO2 was investigated by gas adsorption combined with in situ small angle neutron scattering (SANS). The functionalization was performed by two different methods, (i) grafting and (ii) co-condensation. The adsorbates N-2 at 77 K or a H2O/D2O mixture of 42:58 at 298 K possess neutron scattering length densities (SLD) similar to that of SiO2 and therefore quench the diffraction signals of the nonmodified silica. SANS measurements show that N-2 matches completely not only with the pristine mesoporous Si-MCM-41 but also with Si-MCM-41-SO3H functionalized by grafting. Thus, full access of adsorbate into the entire length of the pores is proven. For the analysis of the distribution of functional groups within the pores in dependence on the used functionalization method, grafting or co-condensation, however, the more specific adsorbate H2O/D2O (42:58) is necessary, because it reacts more sensitively toward small changes in the SLD of the host material. For grafted Si-MCM-41-SO3H materials, an incomplete quenching was observed, indicating that only some regions, probably the pore mouths, have been modified. For a sample functionalized by co-condensation, almost no quenching of the neutron diffraction was found, indicating a very homogeneous distribution of the functional groups along the entire pores.