We comprehensively investigated the characteristics of proteins regulated by miRNAs by performing a protein-domain analysis using bioinformatics techniques. Using several databases, we collected the data on all the domains in the human putative miRNA target molecules. On the basis of these data, we computed the number of putative miRNA targets among the proteins containing the different domains. These domains were classified according to the gene ontology (GO) system. The ratio of the number of putative miRNA targets to the total number of protein types that contained the domains belonging to a GO category was determined, and the domains were analyzed by ABC analysis. These analyses revealed that miRNAs extensively regulate gene expression by influencing the expression of the regulatory proteins involved in gene transcription. Furthermore, many of the genes that encode proteins regulating protein function or cellular processes were putative miRNA targets.