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The biggest loser in Apple’s powerhouse second quarter was by far the iPad, which managed to ship just 4.69 million units when analysts expected somewhere between 6 and 8 million.

During its earnings call today, Apple CFO Peter Oppenheimer made it clear that the company simply couldn’t make enough iPads: “We sold every iPad 2 we could make,” he said.

COO Tim Cook also dispelled assumptions that the Japanese earthquake had anything to do with Apple’s iPad supply trouble, saying on the call that the company “did not have any supply or cost impact” over the last three months. Cook went on to say that Apple will “produce a very large number [of iPads] for the quarter,” but he’s still unsure if that will meet consumer demand.

When asked to elaborate on what exactly is keeping up iPad production, Apple just mentioned that it’s still working through its backlog of production (Cook described it as “the mother of all backlogs”). The company also hinted to another caller that it had trouble projecting production for the iPad versus iPad 2, something that needed to be done well ahead of time.

Apple’s iPad shipments this past quarter were higher than the first two quarters that the iPad was available, but significantly lower than the 7.5 million units that Apple shipped over the holiday period. With the launch of the iPad 2 in March, Apple was definitely aiming higher than last year’s iPad launch with availability in more retails stores in the US, as well more countries internationally. At the end of March, Apple launched the iPad 2 in additional 25 countries, which put an additional stress on demand.

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