An object to be achieved by the present invention is to provide a method for determining the amount of a component contained in a specific lipoprotein fraction in a biological sample using an automatic analyzer, without the requirement of a step of fractionating a sample by centrifugation. The present invention provides a method for separating a target component in a biological sample, which comprises the steps of: (1) causing a biological sample to come into contact with independently dispersed magnetic nanoparticles having a particle size of 50 nm or less, which have anionic functional groups on their surfaces, so as to form an agglutinate of the magnetic nanoparticles and biomolecules capable of interacting with the magnetic nanoparticles; and (2) collecting the agglutinate by an external magnetic field.