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A big part of that loss was due to the acquisition of aQuantive. There was a $492 million dollar loss, but that largely sprung from a $6.2 billion write down of aQuantive, so really it was a one time accounting write off of some of the value of MS's online advertising business. Even for Microsoft, $6.2 billion is a lot of money, but don't expect to see recurring losses like this one in the coming quarters.
Also, there are some big things happening. Servers and Tools alone generated $18.7 billion in revenue last year, so it isn't as if Microsoft doesn't have some serious capital generating assets. Azure is very important to Microsoft in the long term, and I don't see any serious problems there. Windows 8 could be huge (or not), so that remains a question. If I had to bet, I would wager Windows 8 will be a significant and successful version of Microsoft's OS. We shall see.