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After being brought up through the OFI Crete youth system, Kounenakis became one of the youngest players to ever debut in the Greek first division when he debuted at age 17. The central defender had a five-year stay with the Greek Super League club where he earned experience in notable European competitions including the Intertoto Cup and the UEFA Cup. His first career goal came in a 3-0 victory over Hungary’s Ferencvaros in the first round of the 1997-98 UEFA Cup.
After a transfer to Anderlecht in Belgium, where he and teammate Yarris Anastasiou became the first Greek players to win a championship abroad, and a short stretch at Dutch squad Roda JC, Kounenakis returned to OFI Crete where he became a mainstay on their backline over the next seven seasons, culminating with being named team captain from 2007-2009. During his final season at OFI Crete, Kounenakis played against current Kansas City Wizards midfielder Craig Rocastle who also played in the Greek Super League for Thrasyvoulos Filis.
Kounenakis recorded 174 total appearances for OFI Crete, scoring five goals. He then continued his career at Aris Limassol of the Cyprus first division, making 17 appearances and helping the club reach the semifinals of the Cyprus Cup.
Kounenakis joins a short list of Greek players to be signed by MLS, a group that also includes Kansas City Wizards original Frank Klopas (1996-97). Born in Port Elizabeth, South Africa, he speaks English, Greek, and Dutch.