Abstract. We describe the effect of the 6 November 2001 magnetic storm on the low latitude thermospheric composition. Daytime red line (OI 630.0nm) emissions from Carmen Alto, Chile showed anomalous 2-3 times larger emissions in the morning (05:30-08:30 Local Time; LT) on the disturbed day compared to the quiet days. We interpret these emission enhancements to be caused due to the increase in neutral densities over low latitudes, as a direct effect of the geomagnetic storm. As an aftereffect of the geomagnetic storm, the dayglow emissions on the following day show gravity wave features that gradually increase in periodicities from around 30min in the morning to around 100min by the evening. The integrated dayglow emissions on quiet days show day-to-day variabilities in spatial structures in terms of their movement away from the magnetic equator in response to the Equatorial Ionization Anomaly (EIA) development in the daytime. The EIA signatures in the daytime OI 630.0nm column-integrated dayglow emission brightness show different behavior on days with and without the post-sunset Equatorial Spread F (ESF) occurrence.