Structure of the quasi-2-day wave (Q2DW) in the mesosphere and lower thermosphere (MLT) was compared between the northern and southern hemispheres, employing temperature and geopotential height data obtained from the Microwave Limb Sounder (MLS) onboard NASA’s Earth Observing System (EOS) Aura satellite. The Q2DW in horizontal winds was derived using balance equations with MLS geopotential height data. Amplitudes were maximized at ~40° in summer with larger amplitudes in the meridional wind than the zonal wind in both hemispheres, but with much larger amplitudes in the southern hemisphere and a longer duration of enhancements in the northern hemisphere. Weaker enhancements were exhibited in winter in both hemispheres, but maximized at higher latitudes only in the southern hemisphere meridional component. Responses were moderately enhanced from late April to early May only in the southern hemisphere. The westward propagating zonal wavenumber 3 (W3) was largest in summer in both hemispheres, but the Q2DW comprised superposition with other modes in winter. Eliassen-Palm fluxes were derived for each mode. In the southern hemisphere, W3, W2, and W1 in January exhibited upward fluxes at lower latitudes, poleward fluxes at lower altitudes and equatorward fluxes at higher altitudes. A W3 mode in July in the northern hemisphere, on the other hand, exhibited upward and poleward fluxes in the entire altitude range. The Q2DW balance winds were compared with the radar winds. They agreed reasonably in amplitude and phase in summer in the southern hemisphere and lower latitudes in summer in the northern hemisphere and in winter hemispheres.