Provided is a separation container capable of preventing contamination by unnecessary components and capable of efficiently separating target matter. The separation container for separating target matter from a sample has an outer container, an inner container, and a lid section and is characterized by: the outer container having a closed-end tube shape, with the top end open and the bottom end closed the inner container having a tube shape with both the top end and the bottom end open and being arrangeable inside the outer container when both the outer container and the inner container are lined up in the vertical direction the area below the inner container inside the outer container, when the inner container is arranged inside the outer container, being a section for housing sediment from the sample the lid section being removable from the top end open section of the inner container and the inside of the inner container being liquid tight when the lid section is mounted to the open section of the inner container.
