[1] During his career in the NBA, Nesterović played for the Minnesota Timberwolves, San Antonio Spurs, Indiana Pacers, and Toronto Raptors.

The summer of 1996 off season brought another significant feat for Nesterović; while playing for Slovenia's youth national team he was named the MVP at the 1996 FIBA Europe Under-20 Championship.

[6] The exposure on the biggest European stage led to a big time move for Nesterović to the Italian League power Virtus (Kinder) Bologna during the summer of 1997.

[8] He helped Virtus win the EuroLeague title, playing alongside legendary players such as Sasha Danilović, Zoran Savić, and Antoine Rigaudeau.

His best season with the Timberwolves was 2002–03, when he averaged 11.2 points and 6.6 rebounds per game, earning himself a 6-year contract with the San Antonio Spurs in 2004.

Although the Timberwolves were offering him a contract worth $12 million more, Nesterović opted for the move to Texas for a shot at the NBA title.

Nevertheless, he remained the starting center for the majority of the season, and, along with his colleague from the Slovenian national basketball team, Beno Udrih, he ultimately won an NBA title with the Spurs that year.

On June 21, 2006, Nesterović was traded to the Toronto Raptors along with cash in exchange for Matt Bonner, Eric Williams and a second round pick in the 2009 NBA draft.

[14] For the 2010–11 season Nesterović returned to Europe, when he signed a two-year contract with the Greek League powerhouse Olympiacos.