The linear theory of the gradient drift instability in the E and F region ionosphere, including intraionospheric coupling effects, is developed. It is found that when intraionospheric coupling effects are included the instability onset criteria are modified depending on the ratio of the integrated conductivities in the region of the instability onset to the neighboring altitude regions. New results are found for the growth rates of the gradient-drift instability in (1) the F region with inhomogeneous E region coupling and (2) the E region with inhomogeneous F region coupling. The instability growth rate in the F region case is modified as a function of and , where ∑PO and ∑HO are the equilibrium integrated Pedersen and Hall conductivities respectively, and superscripts E and F refer to the ionospheric regions. For P ≫ 1 and Q ≫ 1, modes in the F region are modified significantly by the E region coupling effects, whereas in the opposite limit, the usual results for the local stability analysis of the F region gradient drift mode are recovered, especially at small wavelengths. For the E region gradient drift modes, F region coupling effects have an important influence on the instability for Q ≪ 1, especially at longer wavelengths, while for Q ≫ 1, the instability characteristics are relatively unaffected by the coupling effects. In addition to the well-known reductions to the growth rate proportional to the conductivity ratio of the two regions, we find that the contributions from the inhomogeneous E region ( F region) may be destabilizing under certain conditions and may well overshadow the reductions in the growth rate for the instability in the F region (E region). This effect is found especially important for the F region gradient-drift instability. Among the consequences of the coupling on the local instability process, it is found that the unstable modes may show a rotation of the wave vector with respect to the E×B drift, and the growth rate for the instability has a peak as a function of the wavelength. The results are discussed in light of observations of long-wavelength irregularities in the E and F regions.