A method of preparing siRNAs for selective inhibition of target mRNA isotypes comprises: dividing target mRNA isotypes intended to inhibit the expression thereof and non-target mRNA isotypes from the mRNA isotypes of a gene; allotting a common location information region (A) of exons on genome DNA corresponding to the target mRNA isotypes; allotting a location information region (B) present specifically in exons of genome DNA corresponding to target mRNAs by excluding the location information region of exons on genome DNA corresponding to non-target mRNA from the location information region (A); determining base sequences in the target mRNAs corresponding to the location information region (B); and obtaining siRNA sequences for inhibiting the determined base sequences specifically. The method of the present invention can be used to prepare siRNAs for selective inhibition of specific target mRNA isotypes in a gene having several isotypes by alternative splicing, and enables siRNA design for all the genes in genome, making good tool for functional genomics study.