A method for filtering a protein-containing liquid containing protein at a concentration of 20 mg/mL or more and 100 mg/mL or less, the method including a prefiltration step of filtering the protein-containing liquid by a prefilter having a pore size of 0.08 μm to 0.25 μm and including a hydrophobic resin, and a virus removal step of filtering the protein-containing liquid by a virus removal membrane including a synthetic polymer, after the prefiltration step, wherein the protein-containing liquid before conducting the prefiltration step includes 0.25 g or more of a trimer or higher multimer of the proteins having an average diameter of less than 100 nm, per 1 m2 of the virus removal membrane.