To provide a device for operating magnetic particles capable of treating large quantity, and retaining a gel-like medium layer stably, a vessel is formed so that an area perpendicular to a longitudinal direction in a large-diameter part packed with a liquid layer is larger than an area perpendicular to the longitudinal direction in the small-diameter part packed with a gel-like medium layer. Therefore, in the vessel, it is possible to reduce the diameter of the small-diameter part while keeping the capacity of the large-diameter part large. As a result, in the vessel, it is possible to treat large quantity in the liquid layer, and it is possible to retain the gel-like medium layer stably.