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ipadoct13Microsoft is aiming to protect its turf inside large businesses with the help of Windows tablets that run Office, but a new statistic demonstrates the size of the challenge facing the company.

During Apple’s quarterly earnings call this afternoon, CEO Tim Cook said that 90 percent of tablet activations in the enterprise are iPads, despite the features offered by the Microsoft Surface, as well as other tablets running Windows 8. In addition, Cook said that 98 percent of companies in the Fortune 500 are using iPads.

Cook said he expects Apple to continue to grow in the enterprise.

“I think the road in enterprise is a longer one. The arc is longer than in consumer, which can immediately go out and buy things,” he said. “But I think we’ve done a lot of the ground work … and I would expect that it would have more and more payback in the future.”

The momentum comes in conjunction with Apple’s announcement today that it sold 26 million iPads last quarter, breaking the company’s record for most iPads sold in a single quarter.

Apple certainly has an advantage because it was an earlier entrant into the tablet market. The popularity of the iPad among consumers has increasingly spilled over into the corporate world, which has traditionally been a Microsoft strength.

That’s bad news for Microsoft, which has held off on offering a version of Office for the iPad in an attempt to lure users away from Apple’s platform and towards Microsoft’s offerings. While Microsoft remains confident that business users will still want Office, Apple is pushing to expand the penetration of its iWork productivity suite by giving it away for free with new iOS devices and Macs.

In addition, Apple is pushing to improve the compatibility between Office and iWork, so that it’s easier for people to go without Office on their iPads. While it’s completely understandable that Microsoft would want to leverage Office as a key way to differentiate the Surface from the iPad, that choice may not pay off in the long run if Surface and other Windows tablet sales don’t pick up.

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