A thermal instability leading to the filamentation of auroral electro-jet currents and giving rise to purely growing magnetic field-aligned density irregularities in the E region of the high-latitude ionosphere is investigated. The physical process of the instability is through the modification of the electron-neutral collision frequency due to the electron temperature perturbation in the electrojet. A dispersion relation of the instability is derived, from which the threshold electrojet current and the growth rate of the instability are determined. It is found that they become independent of the scale sizes of the irregularities for scale sizes larger than about 13 m. The proposed instability can, thus, be considered to be one of the mechanisms responsible for those observed relatively large-scale E region irregularities (Pfaff et al., 1984). ¿ American Geophysical Union 1988