Nikolaidis started his youth basketball career in Greece, with HAN Thessaloniki. In 1995, he transferred to the Greek Basket League club PAOK Thessaloniki, where he played for five years. With PAOK, he also played three seasons in Europe's top level competition, the FIBA EuroLeague (1997–98, 1998–99, 1999–00). Moreover, Nikolaidis also won the Greek Cup title with PAOK, in 1999.
