I assume you have created a div that contains controls relating to the users inbox, or a custom message.
Firstly, I suggest putting the controls in an asp:Panel, and not a . This is so you can hide and show the panel at any time.
Force the panel to be hidden on page load. Then, create a method in Page_Load or Page_Init to check when the user has a Message. If so, make the panel visible.
I am assuming you have the messages stored in some kind of DB (Database). If so, create a new column to the PrivateMessage table to save weather the user has read the PM or not. This will allow you to easily distinguish when to show the asp:Panel.
Use a float tag for the asp:Panel, then position it wherever you want it on the screen.
Without any of your source, or any information, this is the best I can give.
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solved Auto Hide/Show DIV in asp.net [closed]