A device for manipulating magnetic particles includes a gelled medium layer and liquid layers alternately stacked in a tubular container along a longitudinal direction of the container. A magnetic particle movement portion for moving magnetic particles exists along an inner wall surface of the container, and the magnetic particle movement portion extends along the longitudinal direction of the container. At a portion where the gelled medium layer is loaded, the cross-sectional shape of the container inner wall in a plane perpendicular to the longitudinal direction of the container is non-circular, and the shape of the magnetic particle movement portion in the cross section is a curved shape or an angular shape.