To provide a method for detecting a deletion in a nucleic acid sequence, capable of examining the gene deletion simply and in a good accuracy on many specimens in a good efficiency.

This method for detecting the gene deletion is provided by using an oligonucleotide primer containing at least continuing complementary 2 bases in 5' side or 3' side of the deleted sector of the nucleic acid sequence, and also the oligonucleotide of which at least one base is a mismatch with a target nucleic acid sequence. It is possible to amplify only the nucleic acid having the gene deletion specifically, and can be utilized as a detection kit of the nucleic acid deletion.

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