Provided is a method for detecting a target nucleic acid, comprising amplifying a target nucleic acid from a nucleic acid sample using a set of primers comprising at least one primer having a tag sequence at its 5′ end and a target binding sequence at its 3′ end; hybridizing the resulting amplified products with detection probes labeled with a label, the detection probes being capable of specifically binding to the tag sequence; hybridizing the hybridization products with capture probes immobilized on a microarray, the capture probes being capable of specifically binding to the target nucleic acid and not to the tag sequence; and determining the results of hybridization.