We present in situ and ground-based measurements of the ratioκof ion cyclotron angular frequency to ion-neutral momentum transfer collision frequency to investigate ionosphere-thermosphere (IT) coupling in the auroralE region. In situ observations were obtained by NASA sounding rocket 36.234, which was launched into the nightside E region ionosphere at 1229 UT on 19 January 2007 from Poker Flat, AK. The payload carried instrumentation to determine ion drift angle and electric field vectors. Neutral winds were measured by triangulating a chemical tracer released from rocket 41.064 launched two minutes later. κis calculated from the rotation of the ion drift angle relative to the E-cross-B drift direction in a frame co-rotating with the payload. Between the altitudes of 118 km and 130 kmκ increases exponentially with a scale height of 9.3 ± 0.7 km, deviating from an exponential above 130 km. κ = 1 at an altitude z0 of 119.9 ± 0.5 km. The ratio was also estimated from Poker Flat Incoherent Scatter Radar (PFISR) measurements using the rotation of ion velocity with altitude. Exponential fits to the PFISR measurements made during the flight of 41.064 yield z0 = 115.9 ± 1.2 km and a scale height of 9.1 ± 1.0 km. Differences between in situ and ground-based measurements show that theE region atmospheric densities were structured vertically and/or horizontally on scales of 1 km to 10 km. There were no signs of ionospheric structure in ion density or ion temperature below scales of 1 km. The observations demonstrate the accuracy with which the in situ and PFISR data may be used as probes of IT coupling.