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SQL Server case insensitive

http://msdn.microsoft.com/en-us/library/ms179254.aspx

Will this work for all databases or must I manually use on every new database which I will add?

Quote from the link you provided, first line reads:

The server collation acts as the default collation for all system databases that are installed with the instance of SQL Server, and also any newly created user databases.

That's assuming the databases being created aren't specifying what collation to use.

A database is a group of objects (tables, functions, etc), which can be from multiple schemas. The instance is the server application running on the host -- you can have more than one SQL Server instance running on a single host. Each could have numerous databases with them.

During the installation of SQL Server you specify the default collation - which is used on every database you create. If you newly create a database and want to have a new collation - you have to specify it according to this documentation-link or in the properties-menu of the database. If you already have created a database and need to change the collation of existing columns filled with data you need to perform this statement.

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