One of the major difficulties faced in the molecular imprinting of proteins is the inherently fragile and flexible nature of the protein template which makes it incompatible with most polymerization systems. Miniemulsion polymerization is a possible approach for preparing molecularly imprinted nanoparticles, and in this study, the method of initiation, the high-shear homogenization, and the surfactant used for the polymerization reaction had been considered as possible factors that can denature the template protein, ribonuclease A (RNase A). The conformation of the protein in a miniemulsion was studied using circular dichroism (CD). It was found that redox initiation was more suitable for protein imprinting and that the addition of poly(vinyl alcohol) (PVA) as a co-surfactant had proved to be effective in preserving the template protein structural integrity. On the basis of the results of the study, polymeric nanoparticles imprinted with RNase A were prepared via miniemulsion polymerization using methyl methacrylate (MMA) and ethylene glycol dimethacrylate (EGDMA) as the functional and cross-linker monomers, respectively, with the conditions of the polymerization system optimized to best preserve the integrity of the protein template. In the subsequent investigation for the recognition properties of the prepared nanoparticles through batch and competitive rebinding tests, the imprinted nanoparticles prepared through the conventional (nonoptimized) miniemulsion polymerization lacked the target specificity as displayed by those prepared under the optimized conditions. This illustrated the importance of protein structural integrity in protein imprinting.