To provide a method for polynucleotide assay enabling easy and quick assaying independent of length, etc., of the polynucleotide.

The method for polynucleotide assay which includes hybridizing fine particles (PG) having polynucleotide adhered thereto and the polynucleotide (HP) containing a hydrophobic group, observing whether fine particles (PG) having polynucleotide adhered thereto are agglomerated or not, and determining the base arrangement in the polynucleotide (HP) containing a hydrophobic group and the base arrangement in the fine particles (PG) having polynucleotide adhered thereto are complementary or not.