OP: Is your company publicly traded? Does it have shares that trade on the NYSE, Nasdaq, etc.? If so, then you can deposit the shares with your broker (assuming you have one), and they will credit your account with teh shares. This is called "holding in Street name," which means as between the company and you, all they know is that your broker holds a hold bunch of shares and not how many each of the broker's individual clients owns. The reason to do this is so that you don't have to keep track of the certificates. Most securities are held this way now, and it really does help to hold them at the broker so that, for example, if your company is involved in a merger the brokerage firm will take care of making sure all of its cleiants, including you, get whatever compensation they are supposed to from that. Otherwise, if you somehow miss the notices about it and don't turn in your shares, after a certain amount of time your shares will not be worth anything.
If your company is not publicly traded, then you should lock them up in a fire proof box or a safe deposit box as a PP suggests. If there is no trading market for the shares, then you will not be able to sell them easily and it is extremely hard to know what they are worth. If you have a broker or a tax accountant, they may be able to advise you better. Some companies that are too small to trade publicly trade through local brokerages, and some don't trade at all. I would look at how your company is set up (is it a corporation? is there a shareholder's agreement? and so on) to figure out what rights you have as a stockholder.
Good luck!
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