The researches on d-hydantoinase activity and substrate specificity towards dihydropyrimidine and hydantoin derivatives have been carried out intensively over the last few decades. So far, the major efforts have focused on (R,S)-5-phenylhydantoin and (R,S)-5-(4-hydroxyphenyl)hydantoin, the most desirable d-hydantoinase substrates from pharmaceutical industry point of view. However, it was shown that d-hydantoinase is a substrate-dependent enzyme, and its activity and stereoselectivity towards 5-monosubstituted hydantoins varied significantly with the type of substrate and the source of the enzyme. The aim of this study was to estimate the substrate specificity of d-hydantoinase towards series of 5-benzylhydantoin derivatives with halogen and methyl substituents in the phenyl ring. The biotransformations were carried out by using commercial enzyme: immobilized, recombinant, cloned, and expressed in Escherichia coli d-hydantoinase from Vigna angularis (rD-HYD). All reactions were monitored by capillary electrophoresis (CE), and the conversion yields were calculated. Additionally, enantiomeric ratios of the obtained d-phenylalanine derivatives were estimated by chiral high-performance liquid chromatography (HPLC). Interestingly, the differences in the activities of examined enzyme towards particular 5-benzylhydantoin derivatives were observed. CE was also shown as a promising method for monitoring the hydrolysis of new substrates by d-hydantoinase and further analyzing of enzyme substrate specificity.