The Vatican bank is checking the account of every client including Holy See employees.
Its new president, Ernst von Freyberg, said it is part of a campaign to root out any money laundering.
Mr Freyberg's predecessor was dismissed for poor management, and the Vatican's financial watchdog said last week it was investigating six possible attempts to use the Holy See to launder money in 2012.
In an interview published in Corriere della Sera, Mr Freyberg said the Institute for Works and Religion - the bank's formal name - was reviewing each of its 18,900 clients.
This was to verify their right to an account and to lay bare any suspicious aspects.
The IOR was combing through about 1,000 accounts a month, he said, to pinpoint owners and who has signature authority.
"This is a system of zero tolerance," he said.
"No suspect transactions, no improper clients and a willingness to contest anyone who is involved in improper activities, even if they are our own employees."
The bank mainly handles funds for Vatican departments, Roman Catholic charities and orders of priests and nuns worldwide but has been used improperly by third parties in the past.
The Vatican is trying to meet international standards on fighting terrorism financing, money laundering and tax evasion, but the European anti-money laundering committee said in July that the IOR still had some way to go.
The Vatican has pledged to make changes and will present a progress report in December.
Freyberg said the bank made a profit of €86.6 million in 2012, up from an average of €69 million annually in the previous three years.
This is believed to be the first time profit figures were given.