In this paper, the analysis of geomagnetic effects on measurements, made by Global Navigation Satellite Systems (GNSS), relies on both the contribution of the geomagnetic field to the refractive index of ionospheric plasma and the presence of field-aligned random irregu- larities. The paper reports results of exploration of the possibility for simultaneous removal of first- and second-order errors by modifying the ionosphere-free combination of dual-frequency measurements. The geomagnetic field affects not only the refractive index but also the structure of ionospheric irregularities. Afraimovich et al. (Advances in Space Research, 2011, Vol. 47, 1674–1680) based on the dependence of the GNSS phase slips on the angle between the satellite- receiver line of sight (LOS) and the magnetic field line, have revealed an anisotropy effect of ionospheric irregularities. To analyze the role of this effect on GNSS measurements, we used nu- merical simulation for studying anisotropy effects of ionospheric irregularities on the probability of occurrence of slips in phase measurements. The simulation results allow us to study and ac- count for the factors which mask effects of this anisotropy. In the future, we are going to exploit this method for estimating the degree of elongation of irregularities to monitor parameters of ionospheric irregularities in the Arctic region.