An apparatus for separating magnetic particles from a liquid which contains said particles, said liquid being contained in an elongated vessel (11) having a length axis (12), said vessel being arranged in a vessel holder (13) with its length axis (12) in a substantially vertical position, said vessel (11) having a bottom and a tapered cross-section that diminishes towards the bottom of the vessel and a side wall (14) which has an outer surface which forms an angle with the length axis (12) of said vessel (11). This apparatus comprises a magnet (15) having a plane outer surface (16) and being adapted for being moved by transport means (17) along a motion path (25), said magnet (15) and said transport means (17) being so arranged with respect to said vessel (11) that over a portion of said motion path (25) said plane outer surface (16) of said magnet is in contact with a portion of said outer surface of said side wall (14) of said vessel (11), and transport means (17) for moving said magnet (15) between a first predetermined position and a second predetermined position along said motion path (25).