Koertzen officiated in his first One Day International on 9 December 1992, and in his first Test match from 26–29 December 1992. Both matches were contested between South Africa and India at Port Elizabeth, during the first series in which television replays were used to assist with run-out decisions. Koertzen soon became well known for very slowly raising his index finger to indicate that a batsman was out. He became a full-time ICC umpire in 1997, and was one of the original members of the Elite Panel of ICC Umpires when it was founded in 2002. He went on to officiate in a record 209 ODIs - becoming the second umpire to stand in 150 ODIs with the match between India and Pakistan at Abu Dhabi on 19 April 2006, surpassing Shepherd's record of 172 ODIs with the Cricket World Cup match between the West Indies and England in Barbados on 21 April 2007, and standing in his 200th ODI with the match between Ireland and Kenya at Dublin on 11 July 2009. He also became the second umpire, after Steve Bucknor, to stand in 100 Test matches with the second Test of the 2009 Ashes between England and Australia at Lord's on 16 July2009, and eventually officiated in 108 Tests. Koertzen was appointed to several high-profile matches, including India-Pakistan series and Ashes series. In both the 2003 and 2007 Cricket World Cups, he officiated on-field in one of the semi-finals and was the third umpire in the final. He was also one of the on-field umpires for the final of the ICC Champions Trophy in both 2004 and 2006, and was selected to umpire in the ICC SuperSeries in 2005, along with Simon Taufel, Aleem Dar and Darrell Hair. His professionalism saw him through some controversial moments: in September 1999 he refused a bribe to fix the outcome of the final of the Coca-Cola Singapore Challenge between the West Indies and India, and in January 2000 he stood in the Test match between South Africa and England at Centurion, where both teams forfeited an innings in order to force a result after South African captain Hansie Cronje had been approached by a bookmaker. He was also highly regarded by the players: he was officially voted the top umpire in 2002, and was nominated for the ICC Umpire of the Year award in 2005 and 2006, on both occasions finishing third behind Taufel and Dar. However, he also made a number of high-profile errors - most notably in the ill-tempered Test between Sri Lanka and England at Kandy in March 2001, and in the final of the 2007 World Cup, where his misinterpretation of the rules regarding bad light resulted in him being banned from officiating in the inaugural ICC World Twenty20 tournament later that year. On 4 June 2010, Koertzen announced his decision to retire from umpiring. He stood in his final ODI on 9 June 2010, between Zimbabwe and Sri Lanka at Harare, and in his final Test from 21–24 July 2010, between Pakistan and Australia at Leeds.
