The Assembly of Citizens at the sixth prytaneia (presidency) discussed whether ostracism should, in principle, be applied that year. If the Assembly voted in favour, at the eighth prytaneia every citizen would write on a shard (ostrako) the name of the Athenian he considered deserving of punishment. According to some scholars, there had to be 6,000 citizens present for ostracism to be applied, and the man whose name appeared most often on a shard would be ostracised. According to other scholars, 6,000 shards had to carry his name before an Athenian citizen could be banished.

Once judged, the citizen in question had to leave Athens within ten days and stay away for ten years. After that, he could return, as he was not deprived of his political rights or his property. Aristides (482 B.C.), Themistocles (472/1 B.C.), Cimon (462/1 B.C.) and Thucydides (443/2 B.C.) were some prominent Athenians who were ostracised.