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With .net Framework 4.5 shall i store encrypted connection string into web.config file OR i shall store connection string at Windows Registry and refer that in application?

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This answer probably applies here

The short version is the config file is going to be easier to backup and restore in the event of a failure somewhere, the registry entry is less likely to be accidentally deleted. Both methods have pros and cons.

Security of either of these things is probably comparable. Regardless of which method you choose, some care should be taken to set the proper permissions on either a registry entry or a config file.

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