Results of experiment conducted at Gakona, Alaska, using intensity-modulated HF heating waves of 3.2 MHz to generate geomagnetic pulsations and large-scale field-aligned density irregularities (FAI), are reported. The echo traces of o- and x-mode sounding pulses from 3.53 to 4 MHz were recorded during heater on/off periods. The ionograms showed that only x-mode echo traces were significantly affected by the HF heater. The returns from 3.53 to ∼3.8 MHz disappeared during heater on period and reappeared after heater was turned off. Ray tracings are performed to explore the effect of FAI on the backscattering of o- and x-mode sounding pulses. The drastic difference between the FAI effects on o- and x-mode backscattering trajectories provides a theoretical interpretation of the observation. Geomagnetic pulsations as large as 2.5 nT were also recorded by a Fluxgate Magnetometer. Thermal filamentation of the HF heater leads to the simultaneous generation of FAI and geomagnetic pulsations.