Pilař made his North American hockey debut during the 2001–02 NHL season, playing 52 games for the St. John’s Maple Leafsof the AHL and earning himself a promotion to their parent club, the Toronto Maple Leafs, for the remainder of the season. The following season, Karel’s career was jeopardized when a viral infection attacked his heart and sidelined him on two occasions. However, he fought back from his illness to play in 50 games for Toronto in the 2003–04 NHL season.
With the NHL season canceled in 2004–05, Pilař returned home to play in his home town for Sparta Prague, scoring a career high of 13 goals and helping his club win the Czech Extraliga title. Unfortunately for Pilař, he suffered a relapse of the heart condition that had plagued him three years earlier, forcing him to miss the majority of the next two seasons. Once healthy, Pilař returned to North American ice 2007, playing the final 10 games of the season with the Toronto Marlies of the AHL.
Seeking an opportunity for an NHL comeback, Pilař signed with the Atlanta Thrashers for the 2007–2008 season. After being claimed by the Chicago Blackhawks from waivers during training camp and re-claimed by the Thrashers, he was assigned to their AHL affiliate, the Chicago Wolves. On January 14, 2009 he left Metallurg Magnitogorsk and returned to the Czech Republic, where he signed a contract to play for HC Sparta Praha. Having played for HC Litvínov of the Czech Extraliga as well as HC CSKA Moscow and Lev Poprad of the KHL after that, he signed a half-year contract with Växjö Lakers Hockey of the Swedish Elitserien (SEL) on January 30, 2012.
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