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Earnings and revenue rose sharply over last year but the number of iPhones sold disappointed- and that caused the miss.
Even though it missed expectations, revenue jumped to $28.27 billion and a net profit of $6.62 billion, or $7.05 a share.
Analysts expected the technology giant to earn $7.28 per share on revenue of $29.4 billion.
Tuesday's earnings call is the first since the resignation and subsequent death of former Apple CEO Steve Jobs.
“We are thrilled with the very strong finish of an outstanding fiscal 2011, growing annual revenue to $108 billion and growing earnings to $26 billion,” said Tim Cook, Apple’s CEO. “Customer response to iPhone 4S has been fantastic, we have strong momentum going into the holiday season, and we remain really enthusiastic about our product pipeline.”
CNBC's John Fortt noted that Cook said in a previous guidance forecast that the earnings release numbers would be lower than projections, but Fortt said people don't listen to the forecast because Apple always does better than expected.
Apple stock tanked in after-hour trading, with an initial dip of 7-percent.