The National Meteorological Service (EMY) has warned of storms in central and western Macedonia as well as the Ionian islands on Thursday.
Weathermen also predicted a significant dip in temperatures in northern Greece and snow for mountainous areas.
They said that the bad weather will move to central Greece, Evia, the Cyclades, parts of the Peloponnese and Crete on Friday.
The warning comes after a whirlwind hit the island of Rhodes earlier in the day. Two seaside restaurants in the area of Gennadi were destroyed and cars and trucks were overturned.
Nobody was injured.