Recently, much attention has been focused on the control exerted by the north-south component of the interplanetary magnetic field (IMF) on the nature of large-scale plasma structures in the polar cap ionosphere. In this paper we investigate whether the above IMF control also extends to the small-scale irregularities of plasma density associated with the large-scale structures. For this purpose, we have performed spaced-receiver scintillation measurements at Thule and Sondrestrom, Greenland, using the 250-MHz transmissions from quasi-geostationary polar beacon satellites. Under IMF Bz northward conditions, moderate levels of amplitude (S4 < 0.6) and phase scintillations are observed with highly variable decorrelation times. Spaced-receiver drifts under this situation show dramatic reversals of the true drift of the diffraction pattern from antisunward to sunward with moderate values of the axial ratio ranging between 4 and 12. For southward Bz we detect, in the central polar cap, a series of large magnitude scintillation (S4 ∼ 1) structures drifting at speeds of the order of 500 m s−1 in the antisunward direction indicating the passage of large-scale ionization structures in the F region. In these cases the apparent drift speed of the diffraction pattern can only be determined as the pattern on ground is highly anisotropic (axial ratios 15 to 40) which makes it difficult to determine the true drift velocity. However, with suitable orientation of our antenna baseline we find that the apparent drift gives a fair estimate of the actual velocity. We also demonstrate that when these irregularities associated with the ionization patches in the F region transit across the polar cap and are observed at Sondrestrom, in conjunction with underlying E region ionization caused by auroral particle precipitation (as sensed by simultaneous incoherent scatter radar measurements of densities and temperatures), the irregularity anisotropy is much reduced. This reduction of anisotropy is possibly a result of increased cross-field diffusion due to coupling with the E region having enhanced density. The true drift of the diffraction pattern measured at Sondrestrom on one evening agrees remarkably well with the simultaneous incoherent scatter radar measurements of F region plasma drifts, both sets of drifts showing equatorward and eastward motion varying between 0.5 and 1 km s−1.