[5] He quickly established himself as a regular player for the team and at the age of 22 he won his first silverware by helping Panathinaikos do the double at the 2003–04 season, winning the 2003–04 Alpha Ethniki and the Greek Cup against rivals Olympiacos.

[8] On 11 June 2004, a day before the eventually successful UEFA Euro 2004 campaign for Greece, it was rumored that Seitaridis signed for Portuguese side, and at the time Champions League holders, F.C.

[15][16] Soon however, Seitaridis began to show his discomfort at the club, failing to settle in Moscow,[17] and claimed the reasons he wanted to leave was that the weather was different from his native Greece and that he could not adapt to the cold.

[28] The 2008–09 season did not start well for Seitaridis, as he lost his place in the first team to new signings Tomáš Ujfaluši and John Heitinga, and his heavy contract meant that Atlético was looking to sell him.

[29] Despite that, Seitaridis was a starter in Atlético's opening game, in a 4–0 victory over Málaga CF,[30] and went on to make 14 league appearances that season.

[32] On 10 September 2009, the last day of the Greek transfer period for free agent players, Seitaridis signed a 4-year deal with Panathinaikos, returning to the team after five years.

However, on 21 March 2010, he surprisingly returned to the line-up for the big derby against rivals Olympiacos,[35] and despite their defeat, Panathinaikos managed to end the season positively by winning the double.

The 2010–11 season started well for Seitaridis, being a starter at Panathinaikos' opening league fixture against Skoda Xanthi on 27 August 2010 and giving a good performance.

He also contributed with one assist in Panathinaikos' 2012–13 UEFA Europa League group stage match against Tottenham Hotspur, which ended 1–1.

Overall his contributions for the victorious team were recognised by naming him as part of the 23-man UEFA 2004 All-Star squad, together with fellow Greek players Antonis Nikopolidis, Traianos Dellas, Theodoros Zagorakis and Angelos Charisteas.

[57] Despite concerns about his fitness,[58] Greece national manager Otto Rehhagel called Seitaridis in his 23-man squad for the 2010 FIFA World Cup.