Thermal ion energy distribution functions and local electric and magnetic fields were directly measured for the first time in the ionospheric E region on board rockets which were launched as part of the E region Rocket/Radar Instability Study (ERRRIS) from Esrange, Sweden, in 1988 and 1989 to investigate plasma instabilities in the auroral ionosphere. Measured ion distribution functions were fitted to shifted Maxwellian distributions, and their resulting ion drift velocities were compared with E¿B/B2 velocities from the double-probe electric field observations. The results show that the ion drift direction rotates with respect to the local electric field direction and that the ratio of the magnitudes of the ion velocity to the E¿B/B2 velocity decreases with decreasing altitudes. Using these observations, the quiet time ion-neutral collision frequencies and neutral wind velocities were estimated and found to be consistent with theoretical estimates. However, significant discrepancies between observations and theory are found in the disturbed E region near auroral particle precipitation regions. These data indicate that the auroral atmosphere is significantly perturbed due to Joule as well as particle heating effects.