Steven Sinofsky, Microsoft's head of Windows, has left Microsoft the company said.
He will leave "with immediate effect" just weeks after the launch of Windows 8, the company's touch-focused next generation operating system.
Sinofsky's departure was a big surprise within the industry, but no reason was given for the move by the company.
Julie Larson-Green will be the new head of Windows software and hardware, including the Surface range of tablets. Tami Reller, the company's CFO and CMO, will lead the business of Windows, Microsoft added.
In a statement, Sinofsky said: "It is impossible to count the blessings I have received over my years at Microsoft. I am humbled by the professionalism and generosity of everyone I have had the good fortune to work with at this awesome company."
CEO Steve Ballmer added: "I am grateful for the many years of work that Steven has contributed to the company".
Ballmer said the changes were aimed at strengthening the company's core businesses.
Sinofsky's departure mirrors that of Apple's iOS chief Scott Forstall, who left the firm last month after widespread criticism of its mapping product.