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A new method is presented for the manufacturing of flexible, not buried and thin-walled hollow microstructures from polymer films. This low-cost method seems to be especially suited for the fabrication of plastic microstructures for fluidic one-way applications in the field of life sciences. It is based on a thermoforming process adapted to microstructure technology and is called 'microthermoforming'. Inside a hot embossing press, a heated thin thermoplastic film is formed into the evacuated microcavities of a plate-shaped metal mould using a compressed gas. The film may be heat-sealed on to a thicker plastic film substrate inside the same press without demoulding the thermoformed film. To demonstrate the performance of the new manufacturing method, flexible capillary electrophoresis and cell culture chips from polystyrene, polycarbonate and a cyclo-olefin polymer with 16 and 625 parallel microstructures each, respectively, have been fabricated.