Cyclodextrin glycosyltransferases (CGTases), members of glycoside hydrolase family 13, catalyze the conversion of amylose to cyclodextrins (CDs), circular α-(1,4)-linked glucopyranose oligosaccharides of different ring sizes. The CD containing 12 α-D-glucopyranose residues was preferentially synthesized by molecular imprinting of CGTase from Paenibacillus sp. A11 with cyclomaltododecaose (CD12) as the template molecule. The imprinted CGTase was stabilized by cross-linking of the derivatized protein. A high proportion of CD12 and larger CDs was obtained with the imprinted enzyme in an aqueous medium. The molecular imprinted CGTase showed an increased catalytic efficiency of the CD12-forming cyclization reaction, while decreased kcat/Km values of the reverse ring-opening reaction were observed. The maximum yield of CD12 was obtained when the imprinted CGTase was reacted with amylose at 40°C for 30 min. Molecular imprinting proved to be an effective means toward increase in the yield of large-ring CDs of a specific size in the biocatalytic production of these interesting novel host compounds for molecular encapsulations. © 2010 John Wiley & Sons, Ltd.