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After my internal HDD broke in my laptop, I've tried to install Debian 6.0.6 on my external HDD. Please note that everything runs great when installing Ubuntu, but for some reason while the Grub stage installation occurs in Debian I get an error telling me that there was a fatal error while installing it.

On my second attempt I skipped the Grub installation and later tried to install it from a LiveCD, but it seems to still fail as the problem is that when I run the boot command my external HDD reboots and the whole booting process halts.

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In what disk are you installing grub? If it is the external one, is your bios able to boot from usb? Moreover, when you install it, is the external one view as sda or sdb? – eppesuig Dec 2 '12 at 20:06
As i already wrote it works with Ubuntu, so i have enabled booting from external drive (~usb). Debian detects it as /dev/sdb. The grub needs to be installed on external drive - the same where the Debian is installed. – Lazy Dec 2 '12 at 21:18
Without the actual error message, this is awfully hard to diagnose. – tripleee Jun 6 '13 at 6:53

Did you try this?

Run a Linux Live CD like Ubuntu. Mount your Debian root partition in the external HDD somewhere (in this example /mnt).

Then run:

grub-install --no-floppy --force --root-directory=/mnt
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Isn't Debian using GRUB2 nowadays? – schaiba Feb 4 '13 at 20:45

You may try to solve it in a different way. If both hard drives are 2.5" (most probably they are), remove the case of external HDD and replace the crashed internal HDD with external one. Internal SATA adapter is much faster than USB, and you may try data recovery from the crashed internal drive.

Assuming you have some knowledge about hardware and a little bit courage. Actually I solved my problem this way.

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