According to a latest report released by a group investigating Mt Gox's case, the missing bitcoins were stolen from the exchange over a period of time starting from 2011.
Is this description really accurate? The chart displayed on the above article I posted shows that the coins were stolen (either hacked or not) in two distinct events rather than continuously over the lifetime of Mt. Gox. For example, you can see the lines diverge immediately and instantly after the 424,242 BTC transfer in June 2011 followed by a "slipping" of reserves during the first half of 2012. Then the rest of the trend seems normal, save the two events which caused the line to be much lower than it should be: