In 514 BC, Harmodius and Aristogeiton assassinated Hipparchus, causing Hippias to further harden his attitude towards the people of Athens.

Cleisthenes' plea for assistance was accepted by the Oracle as his family had previously helped rebuild the sanctuary when it was destroyed by fire.

[13] With help from the Spartans and the Alcmaeonidae (Cleisthenes' genos, "clan"), he was responsible for overthrowing Hippias, the tyrant son of Pisistratus.

He also attempted to dissolve the Boule (βουλή), a council of Athenian citizens appointed to run the daily affairs of the city.

[15] Promptly after his instatement as leader, he commissioned a bronze memorial from the sculptor Antenor in honour of the lovers and tyrannicides Harmodius and Aristogeiton, whom Hippias had executed.

In order to forestall strife between the traditional clans, which had led to the tyranny in the first place, he changed the political organization from the four traditional tribes, which were based on family relations, and which formed the basis of the upper-class Athenian political power network, into ten tribes according to their area of residence (their deme), which would form the basis of a new democratic power structure.

[19] D.M Lewis argues that Cleisthenes established the deme system in order to balance the central unifying force that a tyranny has with the democratic concept of having the people (instead of a single person) at the peak of political power.

[19] This and the other aforementioned reforms had an additional effect in that they worked to include (wealthy, male) foreign citizens in Athenian society.

It is also speculated that, in another move to lower the barriers of kinship and heredity when it comes to participation in Athenian society, Cleisthenes made it so foreign residents of Athens were eligible to become legally privileged.

It was the role of the Boule to propose laws to the assembly of voters, who convened in Athens around forty times a year for this purpose.

In 507 BC, during the time Cleisthenes was leading Athenian politics, and probably at his instigation, democratic Athens sent an embassy to Artaphernes, brother of Darius I, and Achaemenid Satrap, of Asia Minor in the capital of Sardis, looking for Persian assistance in order to resist the threats from Sparta.

Nevertheless, the Athenians preferred to remain democratic despite the danger from the Achaemenid Empire, and the ambassadors were disavowed and censured upon their return to Athens.

So they returned to their own country, and were then greatly blamed for what they had done.There is a possibility that the Achaemenid ruler now saw the Athenians as subjects who had solemnly promised submission through the gift of "Earth and Water", and that subsequent actions by the Athenians, such as their intervention in the Ionian revolt, were perceived as a breach of oath and a rebellion against the central authority of the Achaemenid ruler.