Even in the absence of space weather events or significant geomagnetic activity, ionospheric parameters exhibit significant variations. Research results during the last decade convincingly show that large portion of ionospheric variability is related to lower atmospheric processes. To date, the most studied connections between the lower atmosphere and ionosphere include influences of non-migrating diurnal tides and variations during sudden stratospheric warming events. Although such connections are well demonstrated in experimental data, they are still not well described by global circulation models, and exact mechanisms are a topic of active research. Upper atmospheric disturbances due to other meteorological phenomena (ENSO, MJO) are also under investigation. Connecting the state of the troposphere/stratosphere to the state of the upper thermosphere and ionosphere holds a promise of multi-day prediction of upper atmospheric behavior.