Those with Laiki Bank may never see the rest of their savings again, while Bank of Cyprus savers could lose 40% of their money (over and above €100,000).
Worse still, eurozone officials have hinted that any future bailouts are likely to follow a similar pattern, sparking fears about the safety of savers' nest eggs across Europe.
Charlotte Nelson at savings analyst Moneyfacts said: "Savers across the eurozone are beginning to doubt if their savings are actually safe."
Here, we explain what has happened in Cyprus and look at which other eurozone countries could face similar banking crises in the coming months and years.
The Cypriot bailout deal
Under the terms of the new bailout deal, Laiki Bank will close and Bank of Cyprus faces major restructuring.
The good news for smaller savers is that, unlike the bailout proposal rejected by the Cypriot government last week, accounts holding less than €100,000 will not be touched.
The depressing truth for them is that the €4.2 billion in deposits over €100,000 held by Laiki Bank could be wiped out entirely, while larger savers with Bank of Cyprus, face potential losses of between 30% and 40% on deposits over and above €100,000.
Which countries could be next?
Cyprus is not the only eurozone country to be forced to beg for an emergency bailout. Both Greece and Hungary, for example, have found themselves in a similar position over recent years.
However, it is the first one where savers have been left out of pocket as a result of the banks' failure. And unfortunately, it is unlikely to be the last.
Other eurozone members that could be under threat include Malta and Luxembourg, both of which - like Cyprus - have large banking sectors relative to their size, as well as economically unstable countries such as Italy, Portugal and Spain.
Anyone with savings with other eurozone banks is therefore being urged to consider the options and move their savings if they are worried about a particular bank or have more than €100,000 held with any one banking group.