Abstract: According to the present invention, there is provided a method for detecting a sequence of a nucleic acid in a sample which is complementary to a base sequence of a probe nucleic acid which comprises a step of hybridizing the nucleic acid in the sample with the probe nucleic acid, wherein one or more types of bases of the nucleic acid in the sample and/or the probe nucleic acid are chemically modified in advance. According to the method of the present invention, for example, viruses causative of diseases, exogenous genetic substances such as bacteria, or the presence, mutation or expression state of genes carrying particular genetic information of organisms including human, can be detected efficiently.