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I have installed sql server 2008 R2 with default Instance as "MSSQLSERVER" and due to some reasons uninstalled the same through control panel,if i try to install again with Default instance("MSSQLSERVER") it is giving error "Instance name already in use".

Excuse me if it is a duplicate question. Tried for almost 2 hours found this link https://dba.stackexchange.com/questions/40306/how-do-i-remove-a-sql-server-2008-instance-from-command-prompt-w-o-removing-the but no luck.

Appreciate if anyone can help me regarding this issue with out using named instance.Thanks

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Reset to default
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It is likely that the default instance is still present in the registry.

You could try deleting some registry settings to see whether this resolves your issue. Warning: make sure you back them up first in case this does not work and you need to add them back.

Using Regedit, try first to remove the DefaultData and DefaultLog registry values located at the below registry key. If that does not work try deleting the entire key.

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\MSSQLServer\MSSQLServer

If this doesn't work, I'd recommend a complete uninstall and reinstall, especially if this is a production system, as you want to make sure all your registry settings are as they should be.

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Thanks for the reply. I tried removing registry setting of MSSQLSERVER and also uninstalled everything from my dev machine but still problem persists :(
Ok, so it's a dev machine. Are you sure you haven't installed other version of SQL...for example SQL Server Compact, SQL Server Express....if you have installed Visual Studio .Net...you are often asked if you would like to install the Express edition. If so, this could be causing the issue also.
I have sql server 2005 installed in my machine. Not sure it that causing the issue and how to deal it.
That would be the likely cause of your issue. And I am not sure you can do anything about it, as the default instances uses the computer name alone to reference the database. So you could not have 2 databases with the same reference name. You could try messing with ports and ip addresses to try and see if you could get this to work. Here is a starting point - stackoverflow.com/questions/811667/… But this all sounds more trouble than it is worth!
Finally fixed it by following the steps mentioned in this URL intellitect.com/sql-server-2008-install-nightmare . Problem was due to instances were still sitting under registries

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