Theoretical expressions are derived describing the effect of neutral atmospheric motions (prevailing winds, gravity waves, and tides) on observed propagation velocities of type 1 ionospheric irregularities in the equatorial electrojet. The theory takes account of two ways in which the neutral motions may influence the observed plasma wave phase velocities-directly, through their influence on the ion motion, relative to which the plasma waves propagate, and indirectly, through motion-associated temperature perturbations which affect the ion acoustic velocity. The theoretical results together with what little independent information is available on neutral motions within the equatorial electrojet suggest that they should produce variations in the observed plasma wave phase velocities of the order of several percent. Results are shown to be consistent with variations in the plasma phase velocity observed at Jicamarca, Peru.