Nonlinear three-dimensional (3-D) simulations of the gradient drift instability (GDI) are presented for a two-dimensional equilibrium density gradient representing a polar cap plasma patch. The overall evolution of structuring of the plasma patch is influenced markedly by the effects caused by dynamics parallel to the geomagnetic field. The long wavelengths (kLn ≤ 1) are strongly stabilized in the 3-D case, and the nonlinear state is dominated by smaller mesoscales (kLn » 1) (where k and Ln are the mode number and density gradient scale length, respectively). The results provide an interpretation to the observations at the high-latitude ionosphere indicating a generation of mesoscale irregularities associated with the polar cap patches when the interplanetary magnetic field (IMF) BZ is southward and antisunward convection prevails over the polar cap. The polar cap patches are observed to convect to large distances (∼3000 km) undergoing structuring while maintaining their distinct identity. Thus we suggest here that the inclusion of three-dimensional effects is key to a successful interpretation of high-latitude irregularities, as well as a prerequisite for a credible simulation of these processes.