Zeolites and related crystalline molecular sieves can possess catalytically active acid sites, as well as uniformly sized and shaped pores and voids, that allow for their industrial use as shape-selective catalysts(1). Some catalytic reactions that are not mediated by acids (such as oxidation) have also been shown to occur in zeolites in a shape-selective manner(2), but the diversity in active sites in these materials remains restricted. For mesoporous materials(3), the diversity in catalytic activity has been broadened by grafting organosilanes that contain organic functional groups onto the internal pore surfaces(4-6) or by incorporating them into the structure during the synthesis process(7-12). The former approach has not proven straightforward for microporous zeolites because a large fraction of the grafted functional groups become attached instead to the exterior surfaces of the crystal, there there is no shape selectivity(13). The synthesis of zeolites and molecular sieves using organosilanes as structure-directing agents has been accomplished(14),(15), but the subsequent creation of porosity requires the complete loss of the organic functional groups. Here we report a new methodology that overcomes these problems and allows the production of microporous molecular sieves containing organic functionalities within their pores. During the initial synthesis phase, phenethyl groups covalently tethered to silicon atoms are incorporated into the framework. The external surface-bound functionalities and the structure-directing agents residing within the intracrystalline spaces are then removed to create a microporous material. Subsequent sulphonation of the phenyl rings produces intrapore sulphonic acid sites that perform shape-selective catalysis. Different active-site types can be created by attaching other functional groups to the framework silicon, and we therefore expect that our method will lead to the formation of a wide range of shape-selective catalysts.