Molecularly imprinted polymer (MIP) submicron/nanoscale beads selective for L-Phenylalanine (L-Phe) and D-Phe as well as non-imprinted beads were prepared by modified suspension polymerization involving agitation of the reaction mixture at high rotation speed under safe radical conditions. The effects of pH, template and concentration of racemate solution on the performance of the phenylalanine (Phe) imprinted polymeric submicron/nanoscale beads were studied. L-Phe-imprinted submicron/nanoscale beads prepared for the first time by modified suspension polymerization showed enhanced adsorption capacity and selectivity over those of D-Phe imprinted and non-imprinted beads. Maximum adsorption capacity, 0.35 mg/g, and selectivity, 1.62, of L-Phe imprinted submicron/nanoscale beads were higher than the adsorption capacities, 0.30 and 0.19 mg/g, and selectivities, 1.59 and 1.02, of D-Phe imprinted and nonimprinted submicron/nanoscale beads, respectively. FE-SEM analyses revealed that L- and D-Phe imprinted beads were larger (100 nm-1.5 μm) than non-imprinted nanobeads (100-800 nm). 13C CP-MAS NMR spectroscopy helped in correlating the bead sizes and the extent of reaction during polymerization. Similarly, FT-IR study was used for evaluation of structural characteristics of the prepared Phe-imprinted and non-imprinted beads. The preparation of Phe-imprinted submicron/nanoscale beads with improved adsorption and separation properties and the study of effect of template on the size and performance of the prepared beads are suitable from both economical and research point of view in MIP field.