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Hook ’em while they’re young. That could very well be the code-name of a partnership announced today between Microsoft and TechStars, the high-tech incubator which operates programs in Seattle, Boulder, Boston, New York and Texas. As part of an alliance today, Microsoft said that it will offer both graduates and current enrollees of the three-month long startup bootcamp up to $60,000 of free Windows Azure services over a 24 month period.

“We are excited at the opportunity to work together to help startups when they need it most, with the products, resources and connections they need the most,” said Dan’l Lewin, corporate vice president, Strategic and Emerging Business Development at Microsoft.

It is a smart move by Microsoft to try to win the hearts and minds of startups to its cloud-based platform at the earliest stages, an arena that has long been dominated by (Ironically, is located just across the street from the TechStars Seattle office).

Inside TechStars Seattle

And this isn’t the first time that Microsoft and TechStars have joined forces. You may recall that the two organizations came together last year to form a new Kinect Accelerator program where developers can hack away on new applications that utilize the company’s popular technology. (Microsoft and TechStars recently expanded the application deadline for the three-month Seattle program to February 8th).

TechStars itself has been adding on other perks, including more cash. Entrepreneurs who get accepted into the program — and as we’ve noted in the past it is a very small number — exchange six percent of their company’s equity for up to $18,000.

After raising $24 million in funding last year, TechStars announced that graduates of the program would have the option to take an additional $100,000 convertible note. Coupled with the $60,000 in cloud services from Microsoft, TechStars is hoping that it can help give its startup companies a better shot at success as they emerge from the incubator.

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