Within eight days of the battle of Thermopylae, the Persian army was on the borders of Attica. Themistocles managed to convince the Athenians that they should abandon their city and draw up their fleet in the strait of Salamis, by interpreting the words of the Delphic Oracle as meaning that the Hellenes ought to take refuge behind their wooden wall. The Peloponnesians preferred to put up resistance at the Isthmus, but Themistocles threatened that if the allies did not fall in with his tactics, the Athenians would migrate to Lower Italy. It was on the morning of 29th September that the Persians launched their attack, having blocked the through passages of the strait so as to impede the Hellenes' retreat. As Themistocles had foreseen, they were unable to make the most of their fleet's numerical superiority. By taking advantage of the local currents, the Hellenes either rammed the Persian vessels or, having immobilized them, the hoplites attacked their crews. The Persian fleet was eventually routed in disorder, and took refuge in the anchorage at Phalerum.

After his defeat, Xerxes made home for Asia, leaving Mardonius behind to continue the campaign. Mardonius proposed to the Athenians that they ally themselves with him, undertaking to cede to them large tracts of land and economic aid in rebuilding their city. When the Athenians turned this down, in the spring of 479 B.C., the Persians reoccupied Attica. By now the Peloponnesians had fortified the Isthmus and, unafraid of a Persian landing, were not willing to give the Athenians their support. It was only threat that they would accept the Persian proposals which persuaded them to send Pausanias at the head of a Peloponnesian army to central Hellas. Battle was given in the plain of Plataea in September, 479 B.C., since this particular place was, Mardonius considered, favourable to the movements of the Persian cavalry. But the Spartans upset the Persian superiority by retreating to the heights of Cithaeron, and Mardonius' death meant the Persians' disorderly retreat to Phocis.

Moreover, in the summer of 479 B.C., at the urging of an embassy of the Ionians, the Hellenes' fleet attacked that of the Persians, which had cast anchor in the strait between Samos and the Ionian coast. The Hellenes disembarked an army at Mycale. In the ensuing battle, the Hellenes prevailed and the Persian fleet was set fire to, thus giving the signal for a new Ionian revolt. The Spartans and their allies refused to go on with the war, gauging that the liberation of Ionia was an impossibility. The Athenians and their leader Xanthippus nevertheless decided to lay siege to Sestus, in the Thracian Chersonese. The capture of Sestus in the spring of 478 B.C. signals the end of the Persian Wars and the start of Athenian expansion on the pretext of protecting the Ionians. With the opposition about whether or not to continue the war, the internal conflict which was to split the Hellenic cities during the 5th century already becomes transparent.