A method using a primer composition for amplifying a gene region having various variations and a genotype-analyzable sequence in a target gene comprising: (a) preparing a first primer group comprising a plurality of primers specific to a plurality of templates, respectively, each of the templates includes the genotype-analyzable sequence and each of the primers being specific to a variation in the target gene; (b) preparing a second primer group comprising a combination of one forward primer any one reverse primer the forward and/or the reverse primer being designed by selecting one primer having the greatest number of shared bases from the primers of the first primer group and by using the selected primer as a reference for the primers of the first primer group to have the same sequence and length as the selected primer, the forward primer and/or the reverse primer of the second primer group binding specifically to one of the templates and binding to the other of the templates with allowing mismatch of up to three successive bases or 1 to 2 bases in the vicinity of the 3' end of the templates, wherein the primers of the first primer group and the second primer group are complementary to a sequence which flanks the genotype-analyzable sequence; (c) performing a PCR amplification reaction by adding the primers of the first primer group and the combination of the forward primer and the reverse primer of the second primer group to an amplification reactant including at least one polynucleotide template, a DNA polymerase, dNTPs, and a buffer solution, wherein the first primer group is added to the amplification reactent at a low concentration, and the second primer group is added to the amplification reactant at a high concentration as compared with the first primer group; (d) binding each primer of the first primer group complementarily to the corresponding template, amplifying the template and exhausting the first primer group in the initial PCR amplification reaction; (e) performing further amplification reaction by the combination of the forward primer and the reverse primer of the second primer group, using the first amplification products amplified by the primers of the first primer group as templates; (f) obtaining final amplification products each of which has the genotype-analyzable sequence, being amplified to have the same length to each other and to have different nucleotide sequences only in the genotype-analyzable sequence; and wherein the final amplification products have the same length as the first amplification products. (a) preparing a first primer group comprising a plurality of primers specific to a plurality of templates, respectively, each of the templates includes the genotype-analyzable sequence and each of the primers being specific to a variation in the target gene; (b) preparing a second primer group comprising a combination of one forward primer any one reverse primer the forward and/or the reverse primer being designed by selecting one primer having the greatest number of shared bases from the primers of the first primer group and by using the selected primer as a reference for the primers of the first primer group to have the same sequence and length as the selected primer, the forward primer and/or the reverse primer of the second primer group binding specifically to one of the templates and binding to the other of the templates with allowing mismatch of up to three successive bases or 1 to 2 bases in the vicinity of the 3' end of the templates, wherein the primers of the first primer group and the second primer group are complementary to a sequence which flanks the genotype-analyzable sequence; (c) performing a PCR amplification reaction by adding the primers of the first primer group and the combination of the forward primer and the reverse primer of the second primer group to an amplification reactant including at least one polynucleotide template, a DNA polymerase, dNTPs, and a buffer solution, wherein the first primer group is added to the amplification reactent at a low concentration, and the second primer group is added to the amplification reactant at a high concentration as compared with the first primer group; (d) binding each primer of the first primer group complementarily to the corresponding template, amplifying the template and exhausting the first primer group in the initial PCR amplification reaction; (e) performing further amplification reaction by the combination of the forward primer and the reverse primer of the second primer group, using the first amplification products amplified by the primers of the first primer group as templates; (f) obtaining final amplification products each of which has the genotype-analyzable sequence, being amplified to have the same length to each other and to have different nucleotide sequences only in the genotype-analyzable sequence; and