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I have two hard disks, with each hard disk having a single Windows XP system partition installed on it and multiple partitions.

Will there be a single boot.ini for all the hard disks and where will it be (first or second hard disk)?

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Yes, there is a single boot.ini file, usually located in C:\Windows.

You can check it from System configuration Utility: Start menu -> Run and type msconfig.exe

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Short answer: There should be one boot.ini per drive.

Long answer: There should be one boot.ini per drive, along with one bootloader for each drive. The one used is decided by the BIOS's boot order.

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Actually, the boot.ini is located in the root of C: (C:\boot.ini). Also it's a system file so you won't be able to see it unless you enable the option to view System/Hidden files in Explorer (or "dir /ah" via cmd-line). The msconfig utility noted above just lets you see the contents of the boot.ini and change them via a gui instead of having to edit it with something like notepad.

This article http://support.microsoft.com/kb/314081 explains many of the options.

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