Anthony Scott, Microsoft’s (MSFT) veteran chief information officer (CIO) of five years, has left the company for personal reasons, according to a report in GeekWire later confirmed by the vendor in a statement.

Word leaked out of Scott’s departure over the weekend when his LinkedIn profile changed to “former CIO.” Scott’s last day at Microsoft was this past Friday and, according to reports, Microsoft disclosed his plans internally late last week.

“Tony Scott decided to depart Microsoft to focus on personal projects,” Microsoft said, in a statement. “While at Microsoft, Tony was a strong IT leader passionate about taking Microsoft’s technology to the next level and using our experiences and learnings to help customers and partners. We thank Tony for his contributions and wish him well.”

Jim Dubois, Microsoft vice president of IT product and services management, will handle Scott’s duties until a permanent replacement is found, the company said.

Scott said it was his choice to leave Microsoft and that he did so for personal reasons. He elaborated in an email to GeekWire, citing family reasons and saying he will return to work “in some form in a few months.”

Microsoft hired Scott in January 2008 to run its global IT organization, replacing Stuart Scott, who had been fired two months earlier for breaching an unspecified company policy. As a 25-year industry veteran, Scott’s background includes heavyweight stints as senior vice president and CIO at Disney, chief technology officer at General Motors and operations vice president at pharmaceutical company Bristol-Myers Squibb.

A major part of Scott’s job at Microsoft was to oversee the testing of new products internally through the vendor’s massive IT department prior to public rollouts. At the time of his hiring, Microsoft described it as the responsibility to “drive our solutions and deployment throughout our enterprise and provide valuable input and feedback to our product groups.” In addition, Scott oversaw Microsoft's IT department’s critical role in keeping its internal systems operational, up to date and secure.

Microsoft’s TechEd event for IT professionals and enterprise developers is this week in New Orleans.