Provided are a carrier-enclosed transformable container, a carrier-enclosed transformable container processing apparatus, and a carrier-enclosed transformable container processing method about which a carrier to which various substances such as biogenic substances are bonded or bondable is held in a transformable container as the container to be in a substantially stationary state, thereby making it possible to make the handling of the carrier, measurement, and other treatments effective, speedy, and easy. The container is formed to have: a containing part which can contain liquid and gas at its inside surrounded by a wall face, a part of this wall face having a transformable wall face capable of undergoing a predetermined transformation without changing the entire internal surface area of the wall face substantially; an orifice part which is connected to the containing part and can undergo the inflow and outflow of a liquid sucked and discharged by the expansion and contraction of the inside by the transformation of the transformable wall face, respectively; and a carrier to which a predetermined substance enclosed in the containing part to be in a substantially stationary state is bonded or bondable.
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