Amain object of the present invention is to provide a method of preparing a nucleic-acid-containing complex formulation which can be sterilized by filtration and administered intravenously to human, and can retain stability of polynucleotides included in the nucleic-acid-containing complex formulation.The present invention relates to a method of preparing a nucleic-acid-containing complex formulation, comprising the following steps:mixing a solution comprising two separate single-stranded polynucleotides (for example, poly I and poly C) capable of forming a double strand and a solution comprising a cationic carrier or the ingredients thereof to form the cationic carrier, andperforming a dispersion treatment to the mixture.