On 16 June 2006 he was transferred to Atlético Madrid for a fee of €12 million, being the second Greek footballer to play for Atlético after striker Demis Nikolaidis. The latter was the one who convinced him to join the club, together with his ex-Dynamo teammate Costinha who joined Atlético the same year. Seitaridis was sent off in the first half of his debut game, in the La Liga opening match away to Racing Santander on 27 August 2006. On 15 October 2006, he received his second red card only six games into the season, as he was cautioned twice in a home league game against Recreativo Huelva.