We have developed a new beam configuration for monostatic incoherent scatter (IS) radars at high latitudes in order to estimate the vertical component of the neutral wind velocity in the lower thermosphere (from 100 to 120 km). This method has been applied to experiments with the Sondrestrom IS radar, Greenland, on 5 and 8 March 2004. The measurement and the analysis methods provide various temporal and altitudinal structures of the vertical neutral wind velocity with amplitude of a few tens of meters per second at 3 km height resolution. This paper also demonstrates how to evaluate assumptions adopted in calculations of the vertical neutral wind velocity using experimental data on 5 and 8 March 2004. Caution should be exercised in inferring effects of variations in the thermospheric density or the ion-neutral collision frequency in association with vertical thermospheric motions, in particular above 112 km.