An administrator will try to sell its assets, but many creditors, including those who had bitcoins with the exchange, might not get their money back.
After Mt. Gox went offline in February, its CEO, Mark Karpeles, said tens of thousands of bitcoins worth several hundred million dollars were unaccounted for.
Under the bankruptcy proceedings, Karpeles' liability will be investigated, Mt. Gox said in a statement.
Mt. Gox has suggested the bitcoins were stolen. The company has not been able to confirm the bitcoin balances of its users, although they can look at a balance on a website that is no guarantee for a claim, it said.
Bitcoins, created in 2009, are used for transactions across borders without third parties such as banks and have become a popular investment.
Mt. Gox said in a statement that a meeting for creditors will be held in July, and a report of its outcome will be shared on its website for those who can't attend.