How To Align Partitions on an Upgraded iPod Hard Drive in Windows

If you’ve upgraded your iPod using a newer, larger drive, there’s a chance that the new drive uses “Advanced Format” sectors.  Drives that are use Advanced Format have sectors larger than 512 bytes; generally 4K bytes.

If you upgraded your iPod using one of these drives, it will work, but performance will be degraded significantly.  This is because iTunes partitions the drive inside of your iPod with no consideration about whether it is an Advanced Format drive or not.  iTunes uses two partitions when formatting:

  1. The first partition is the “system” hidden partition.  This is where the iPod stores its operating system.
  2. The second partition is free space formatted as FAT32.  This is the partition we are concerned about.

I upgraded my 5G iPod Video 60GB to a 120GB drive using a Samsung HS12YHA, but I was really disappointed when syncing took forever and write speeds were less than 1MB/s.  This occurs when the logical sectors on the disk are unaligned with the physical sectors.  The iPod uses 2K sectors.  Here’s a diagram to show what I mean:

diagram that shows the different between aligned and unaligned sectors

If you take a look at the unaligned picture you can see that when the OS writes to disk (using logical sectors, as usual) it’s possible that the logical sector spans across two physical sectors.   Because a sector is the smallest unit that a disk can address, when a sector is written to the entire sector needs to be read, the change made, and then the sector written back to disk.  As such, if you change a logical sector that spans across multiple physical sectors, then both physical sectors need to be read entirely, changed, and written to disk again causing the drive to do a lot of extra work.

What we want to achieve is a drive that has its logical sectors aligned with its physical sectors.  To do this, the start of the data partition on the iPod needs to start at a physical sector.  Here’s how to do it on Windows.


  1. Restore your iPod using iTunes.
  2. Download Symantec’s Partition Table Editor, PTEDIT32, from this link.
  3. Open PTEDIT and select your iPod from the drop down menu.  You can do this by matching the disk size with your iPod side.  You may have to start PTEDIT as an administrator by right-clicking it and choosing “Run as administrator”.
  4. You now need to figure out which sector partition 2 should start on.  DO NOT alter partition 1!  To determine which sector to use, increase the number in “Sectors Before” for partition 2 until it is divisible by 8.  Keep track of how many sectors you add!  For instance, if your “Sectors Before” field reads 224910 (as mine did) you would increase this to 224912 because 8 divides evenly into it.
  5. Add the same number of sectors to the Starting Sector field for partition 2.  My disk started at sector 1, so I increased this to 3.
  6. Subtract the same number of sectors from the Sectors field for partition 2.  My partition had 234216737 sectors, so I made this 234216735.
    DO NOT alter any other fields!
    Here’s what my final partition table looked like:
  7. Save your changes.  Exit PTEDIT and “safely remove” your iPod.
  8. The iPod should reboot, but it’s probably going nuts trying to understand what happened to the partitions, as you’ve destroyed the file system.  You’ll need to boot the iPod into Disk Mode to continue.
  9. Connect the iPod to the computer.
  10. Download fat32format and extract it somewhere convenient.
  11. Open a command prompt and navigate to the spot where you extracted fat32format.
  12. Make SURE you type this command correctly.  Type:

    fat32format IPOD_DRIVE_LETTER_HERE:

  13. This will quickly format the iPod’s data partition.  When it’s done, continue.
  14. Disconnect the iPod and reconnect it to the computer.
  15. You should now be able to use your iPod at full speed!
As always, if you have any questions, post them here and I’ll do my best to help.