A new synthetic strategy for incorporating controlled amounts of catalytic moieties inside the mesopores of a series of mulifunctionalized mesoporous silica nanoparticle (MSN) materials is presented. By using the method, a new cooperative catalytic system for the synthesis of biodiesel from various free fatty acid (FFA)-containing oil feedstocks is developed. The selectivity of the multifunctionalized MSN catalysts could be systematically tuned by varying the physicochemical properties of the pore surface-bound secondary groups. These different functional groups could cooperatively catalyze both the esterification of FFA and the transesterification of oils with short-chain alcohols (e.g., methanol and ethanol) to form alkyl esters (biodiesel). This is an abstract of a paper presented at the 229th ACS National Meeting (San Diego, CA 3/13-17/2005).