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According to Microsoft here is what Bootrec /FIXBOOT does:

"This option writes a new boot sector to the system partition by using a boot sector that's compatible with Windows Vista or Windows 7"

And this is what Bootrec /FIXMBR does:

"This option writes a Windows 7 or Windows Vista-compatible MBR to the system partition"

Now isn't the MBR just a type of boot sector? What other types of boot sectors would it fix? I'm confused when I would use one over the other- isn't mbr the only boot sector windows uses?

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As I understand it, MBR = First sector on the entire drive and Boot Sector is the first sector in a partition. Your BIOS reads the MBR first then gets pointed to the Boot Sector of the system partition which controls the loading of that partion or will present you with a menu so you can choose another partition to boot off. I think LILO / NTLDR etc reside in the boot sector? – Mark Innsbruck Owen Jul 7 '14 at 14:25
Mark, you're correct - you should answer. – Ryan Ries Jul 7 '14 at 14:37
"MBR = First sector on the entire drive and Boot Sector is the first sector in a partition", but the MBR is a type of boot sector. What type of boot sectors are the ones at the beginning of a partition? Are those the "Volume Boot Records"? – red888 Jul 7 '14 at 14:42
The other thing that confuses me is that it says both commands write to the system partition. So we're talking about the same partition (and I believe you can have only one system partition). When would I ever write a boot sector to the system partition that wasn't an MBR type of boot sector? In Windows land does boot sector have a specifically different meaning than MBR, because everything I read says a MBR is just a type of a boot sector. – red888 Jul 7 '14 at 14:58
up vote 6 down vote accepted

This turned out to be a very interesting question. There are lots of links out there on this topic but they are ambiguous in describing the difference/relationship between the two. Best description I've found of the hard drive configuration for a Windows OS is this one:

It appears that MBR and Partition Table are in the same sector on a drive. The MBR is "smaller" in that it is the very first thing on the drive, that then uses the partition table to continue the boot process to a specific OS. The two command options effectively fix different links in the boot chain:

/fixmbr replaces the information and small executable that reads the partition table to find where the OS may be located. So this exists on any drive that has been formatted and effectively exists to read the next little bit on the hard drive that tells where the/an OS is supposed to be located. In essence, this is not necessarily a Windows-specific item.

/fixboot replaces the next part - the entry in the partition table that points to where the actual loadable executable is located for the OS. So this is fixing the next link in the chain of the boot process. This command does create a windows-specific result in that it reminds the hard drive where to find Windows in particular.

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