Geomagnetic field-aligned (FA) ion motions in the transition region between E and F regions (from 150 to 250 km; hereafter termed the E-F transition region) in the polar ionosphere are analyzed statistically using data from European Incoherent Scatter (EISCAT) radar from 1987 to 1999. We use all available EISCAT data sets that satisfy the definition of data selection criteria (i.e., 24-hour observation periods beginning at 1200 UT); therefore it has not been feasible to investigate seasonal, solar, and geomagnetical activity dependences. FA ion motions above and below the E-F transition region (250--300 km and 100--150 km, respectively) are also analyzed to compare with lower-altitude ion motions in the E-F transition region. The FA ion velocity that is observed with the EISCAT radar can be written as the sum of the FA ion diffusion velocity and FA component of the thermospheric wind using the ion momentum equation. The main purpose of this paper is to understand quantitatively the relative contributions of ion diffusion and neutral wind on FA ion motions in the E-F transition region. We derive the amplitude and phase of the first three daily harmonics, i.e., the 24-, 12-, and 8-hour periodic oscillations in observed FA ion velocities and estimated FA ion diffusion velocities. The spectral characteristics are determined with a Fast Fourier Transfer (FFT) method after averaging velocity data in 1-hour bins. The amplitude of the 24-hour periodic oscillation is the largest of the three harmonic components for the FA ion velocity as well as FA ion diffusion velocity. While the amplitude of the 24-hour periodic oscillation in FA ion diffusion velocity below 230 km is considerably smaller than the values of the observed FA ion velocities, the amplitude from 230 to 300 km is comparable to that in observed FA ion velocities. From 230 to 300 km the phase of the 24-hour periodic oscillation in FA ion diffusion velocity has about 180¿ difference from that in the observed FA ion velocity. This spectral analysis results suggest that, in the E-F transition region, FA ion diffusion velocity is not the major contributor to the three harmonic oscillations in the observed FA ion velocities; thus FA component of thermospheric winds or tides prove to be the primary contributor.