This letter presents for the first time the results of a statistical study that had looked into the dependence of scintillation on the propagation geometry of GPS signals at high latitudes by combining the geometrical parameters, namely elevation and azimuth, along with the magnetic field vector into a single variable called the magnetic field aligned angle (MFAA). An increase in the value of scintillation indices when MFAA approaches zero is observed. This indicates the presence of field-aligned irregularities and the fact that MFAA is sensitive to irregularities whose size extends to Fresnel scales as well. Contrary to previous experimental and modeling studies which have shown higher variations of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\sigma _{\phi }$ </tex-math></inline-formula> index as compared to the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$S_{4}$ </tex-math></inline-formula> index with the propagation geometry of GPS signals, our results suggest that these higher fluctuations in <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\sigma _{\phi }$ </tex-math></inline-formula> were refractive in origin and were the result of improper detrending of the phase at high latitudes where the use of constant cutoff of 0.1 Hz is not accurate due to higher ionospheric plasma drift velocities at these latitudes.