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Wolfgang Niersbach has resigned as president of the German Football Association after a meeting with officials on Monday.
Niersbach is suspected of having known about and assisting with the payment of sums to secure votes for the 2006 World Cup, which was staged in Germany.
An investigation is ongoing, but Niersbach has decided to step down from his position with immediate effect, while he once again stressed his innocence in a statement published on the German FA's (DFB) website.
"I was involved in the bid for the 2006 World Cup from day one until the final documentation of the summer fairy tale was submitted," Niersbach wrote.
"In all of those years, I not only always worked with great passion, but also always cleanly, faithfully and correctly.
"In the areas of marketing, media, accreditations, and event organisation, which I worked in, I can say with a clean conscience that I have absolutely nothing to reproach myself for.
"It makes it all the more depressing and painful for me to be faced with things nine years later that I was not involved in, and which have left many questions open for me.
"I remain and would like to make it clear unmistakably once again that I had absolutely no knowledge of the background of the flow of payments that are being looked into.
"It makes it even harder for me to make the decision to draw political consequences.
"27 years at the DFB were always more than a job for me. The work in a variety of roles was something very dear to my heart.
"I love football and this association, in which I have experienced some wonderful moments and been able to work with some amazing people.
"In order to protect this DFB and the office, it is with a heavy heart that I am resigning as DFB president. At the same time, I will continue to do all I can for a comprehensive clarification of what has happened."
In a statement to reporters at the Frankfurt headquarters of the DFB, the 64-year-old said he had "realised that the time had come to take responsibility for the political events surrounding the 2006 World Cup", and added that "the position of DFB president must not be damaged".