Nanometre-sized structures were fabricated by electron beam-induced deposition in a scanning transmission electron microscope. A small amount of metal-organic gases, W(CO)6 and dimethyl acetylacetonato gold, were introduced near a substrate in the chamber of the microscope. The gas was decomposed by the irradiation of focused electron beams and nanometre-sized deposits containing W or Au were produced. Moving the beam position enables us to produce structures with a variety of shapes. High-resolution electron microscopy observation revealed that the structures consisted of nano-crystalline and amorphous parts.