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The departure has stunned analysts who saw Belluzzo - responsible for overseeing consumer initiatives - as the next chief executive.
Matt Rosoff, Directions on Microsoft analyst, believed he left after failing to meet targets.
All six of Microsoft's business units will now report to CEO president Steve Ballmer, with more responsibility being given to divisions for their own fiscal and operational performances.
The software giant refuted claims that the shake-up would make it easier to split itself into multiple companies.