A method of analyzing a target nucleic acid fragment is provided that is capable of being performed simply and promptly, by anyone, using a compact device without requirement of specific technique or complex operation. The method comprises timely detection of a double-stranded nucleic acid fragment formed during the polymerase extension reaction due to a specific base sequence of the target nucleic acid fragment as increase of an electrochemical response under the existence of an electrochemically active intercalator; and the kit utilizes the method.