The culture filtrate of the fungus, Alternaria alternata, was used for the bio-reduction of sodium selenate to produce selenium nanoparticles. Change in colour to dark red of the reaction mixture signifies the development of nano-α-selenium. Dynamic light scattering experiments, atomic force microscopy, scanning and transmission electron microscopic images explained the formation of monodisperse spherical α-selenium nanoparticles in the range of 30-150nm. X-ray diffraction spectrum of the nano-Se exhibited a broad peak at the 2θ angles of 15-35°, signifying its amorphous nature. Energy-dispersive X-ray study revealed the presence of selenium in the nanoparticles. Fourier transform infrared spectroscopy confirmed the presence of a protein shell outside the nanoparticles, which in turn support their stabilisation. A novel method has been presented here to synthesise nano-selenium in which the fungal culture filtrate was used and up-to-date literature survey showed that this is the first report on mycosynthesis of selenium nanoparticles. © 2011 The Institution of Engineering and Technology.