A nucleic acid sample is mixed with a nucleotide reagent under hybridizing conditions. The nucleotide reagent contains nucleotides each combined at 3'- and 5'-terminals thereof with particles. After cleaving double strands of hybridization products, at least ones of particles separated from each other by the cleaving and particles held in the unreacted reagent and subjected to no cleavage are detected for measuring nucleic acids in the sample. Since the particles separated from each other by the cleaving and the particles held in the unreacted reagent and subjected to no cleavage are different in size of particle masses from each other, these two groups of particles can be discriminated and detected. Therefore, a labeling substance in the unreacted reagent is no longer required to be washed and separated, enabling nucleic acids to be quickly measured with high sensitivity.