To provide a method for separating a non-HDL lipoprotein from a biological liquid avoiding problems associated with a prior art method, more quickly carrying out the separation without using a complex adjunct device, and making the measurement of an HDL cholesterol quicker and simpler.

An HDL lipoprotein in a blood serum is separated by first fractionating a non-precipitating HDL lipoprotein from an LDL lipoprotein, a VLDL lipoprotein, and a chylomicron that can be precipitated by virtue of a precipitant, and subsequently removing the resulting precipitate by a filtering method instead of a conventional centrifugal separation method. A filter made from a hydrophilic ester mixed with cellulose is preferable and one having a pore diameter of not greater than 0.8 m is used. Complex operation and a long operation time associated with a prior art centrifugal separation method can be made simpler and shorter by virtue of using the filtering method.