There were hundreds of Greek city-states scattered around the Mediterranean and Sea littoral from present day Spain in the west to Asia Minor in the east.
The first phase was the Ionian Revolt 499 to 493 BCE involving the city-states of Asia Minor, aided by Eretria and Athens from mainland Greece.
So the answer to the quetion is 'several hundred Greek city states did not take part'. The same answer applies to the subsequent stages of the war.
Athens.
The Persian Empire versus coalitions of Greek city-states led first by Sparta, then by Athens.
There were already over 2,000 Greek city-stares. None was created from the Persian war.
The Persian Empire and the Greek city-state around the eastern Mediterranean littoral.
The Greek city-states of Asia Minor revolted against Persian rule. This war spread to include mainland Greek city-states.
Athens
The Persian Empire and an alliance of Greek city-states led first by Sparta and then Athens.
The Persian Empire versus a coalition of Greek city-states, at first led by Sparta, then by Athens.
The Greek city-states of Asia Minor revolted against Persian rule.
The Persian thought the Persian Empire. The coalitions of Greek city-states thought the coalitions of Greek city-states.
The Persian Empire versus a coalition of Greek city-states led first by Sparta, then Athens.
The Greek tyrant of the Greek city-state of Miletus in Asia Minor persuaded the Persian provincial governor the become involved in an expedition to capture the island city of Naxos The expedition was defeated, and knowing that retribution was coming, he organised a revolt by all the Greek cities in Asia Minor. This Ionian Revolt spread, encouraging the Persians to try to bring all the Greek cities under its control.