This paper reports a practical method of generating circularly polarized terahertz (THz) waves from intrinsic Josephson junctions (IJJs) and controlling their polarization states by external local heating. We theoretically find that a mesa-structure IJJ whose geometry is almost square can emit circularly polarized THz waves by local heating of the mesa. Moreover, we demonstrate that the polarization states of the THz waves change dramatically with the local heating position. Our results indicate that the use of local heating can provide a high level of controllability of the THz emissions and significantly extend the range of applications of IJJ-based THz emitters.Terahertz (THz) electromagnetic (EM) waves have potential applications in a wide range of fields, e.g. nondestructive inspection of materials, medical diagnosis, bio-sensing, and high-speed wireless communication [1]. Toward the realization of a practical THz emitter, various THz sources, such as quantum-cascade lasers and resonant-tunneling diodes, have been studied so far [2,3]. Since the first observation of intense and continuous THz wave emitted from a Bi 2 Sr 2 CaCu 2 O 8+δ (Bi2212) single crystal by Ozyuzer et al. [4], considerable attention has been paid to high-T c cuprate superconductors. A layered structure of Bi2212 single crystals composed of superconducting layers and insulating layers forms a stack of the Josephson junctions whose thicknesses are on the atomic scale ∼ 1.5 nm. Stacks of these natural Josephson junctions, which are referred to as intrinsic Josephson junctions (IJJs), can generate an AC Josephson current in the THz frequency range by application of a voltage, and the THz wave emission is attributed to the generation of this current. Intense THz emissions have been reported for IJJs fabricated in a mesa geometry, which itself behaves as a cavity resonator, and thus, a number of studies on such IJJ mesas have been carried out both experimentally [4][5][6][7][8][9][10][11][12][13][14][15] and theoretically [16][17][18][19][20][21][22][23][24][25][26]. However, in the previous studies, little attention was given to the state of the polarization of the THz waves. Control of the polarization is a fundamental issue for technological applications of THz waves. In particular, the ability to generate and control circularly polarized THz waves would open the way to various applications such as circular dichroism of proteins [27].In this paper, we present a method of generating and controlling circularly polarized THz waves from IJJ mesas by using external local heating. We consider a IJJ mesa whose geometry is almost square and whose temperature distribution is controlled by laser heating (see Fig. 1). We numerically investigate the emission power and the polarization of the THz waves from the mesa by solving the sine-Gordon and the Maxwell equations simultaneously. Interestingly, both the ellipticity and handedness of the THz waves from the IJJ mesa strongly depend on the position of the laser heating. Figure 1 shows a schematic fig...