Helping people with computers... one answer at a time.
Depending on how you look at your disk, the amount of space used can appear quite different. We'll look at some of the possible reasons.
In explorer, under the properties of the "C" drive, the space USED is 70 gb. All folders are shown, and by selecting all the files and folders on the drive contents and properties, I get 31gb used. I can not find the other files anyway.
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It's worse than you think. Just with a little poking around I was able to generate several different numbers for the "spaced used" on my hard drive.
I'll admit, it's frustrating. Fortunately it's not something we need look at very often, but you'd think the line between what's used and what's not used would be clear. Actually it is, but there are different ways of looking at "what's used" that don't tell the whole story.
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First let's look at the two examples mentioned in the question. Here's Windows Explorer's view on my C: drive, by right-clicking on the drive and clicking on Properties:

As you can see, Explorer reports that about 47.8 gigabytes are in use, and that 24.6 gigabytes is available as free space. If you're just wondering about the free space on the drive, or how much of the drive is in use, these are actually the numbers I'd use - they take pretty much everything into account.
Now, back in Windows Explorer's view of my C: drive:

Click on any file at the root of C:, and type CTRL+A to select All files. Now, right click on any of the files selected and click on Properties:

You can see that Windows reports the size of all files in C:\. It reports both size, and something called "size on disk". And neither are the close to the 47.8 gig reported to be in use earlier.
Let's clear up "size on disk" first. Windows allocates space for files in "clusters" or "allocation units". The size of a cluster varies, but ranges from 512 bytes to 32K or more. On my C: drive the allocation unit is 4096 bytes. What this means is that Windows will allocate 4096 bytes for any file or portion of a file that is from 1 to 4096 bytes in length. A 1 byte file? That takes up 4096 bytes "on disk". 100 byte file? Still takes up 4096 bytes on disk. A 4097 byte file? That takes up 8192 bytes - one complete 4096 byte cluster, plus another 4096 byte cluster to hold the extra byte.
So in determining how much disk space is used by the files, we need to pay attention to the larger "Size on disk" number.
But that number is still very different than the 47.8 gig.
There are a number of issues that contribute to the difference:
Hidden and System Files - The Windows Explorer display above was using the default settings which do not display files marked as "hidden" or "system", and as a result they are not included in the calculation. Changing that setting increases the "Size on disk" by approximately 7 gigabytes as all the hidden files on my machine were included in the calculation. Most notably that included the system swap file and hibernation file, both of which are large, and marked as hidden.
Directories - directories, or the lists and indexes of the files on your machine, are not files themselves, but they do take up space.
The File Allocation Table or Master File Table - The FAT itself, of FAT file system fame, is actually pretty small. The MFT however, used in NTFS file systems, is also stored on disk but not visible as a file. It defines where the used and free space on a disk actually is. Depending on the size of your disk, your files, and the size of the allocation unit, the MFT can be quite large.
The Log File - it's a file, but again, you won't see it. This is internal NTFS data.
There's probably much more that I'm not aware of that enters into the picture as well. I know in researching this issue there was no way I could actually get all the numbers to add up. Possible additional culprits further confusing the situation include compressed files (which appear bigger than they really are on disk), junctions and shortcuts which may or may not be counted as files, utilities which may or may not include the recycle bin as part of the "spaced used" since the contents have technically been deleted, and Windows Vista's ability to keep additional versions of files automatically (though where they're kept and how they're managed, I'm currently not sure).
So yes, it is confusing.
But as I said earlier, I would rely on the drive properties to tell you about the actual used/unused state of your drive.
Article C3122 - August 19, 2007 « »
August 12, 2012 9:44 AM
I have two external hard drives [Toshiba and Lacie] for backup purposes so I can have one on and off site at all times in rotation. I've just copied contents between them and individually all files are equal size, but in windows explorer the drives' 'used spaces' differ by a margin of about 1percent. A mystery as I have emptied recycle bins for each. Maybe each drive has differing system files. There is opportunity to 'clean up system files' but I do not dare to do that without knowing more. I am not bothered except that it would be useful if the sizes tallied because then individual files and folders would not need to be checked which can be too time consuming.
January 11, 2013 4:12 PM
Hi, I am facing same problem in portable hard drives. I have three 1TB portable hard drives and loosing 2 -3 gb on two drives and 100 gb on third drive....I have done everything........I checked online also for the solution but there is nothing...Only this article was good. others have just written for the sake of writing.........Few months back I had same problem with my one portable drive. At that time i formatted the drive and got my space back.......but this time all my drives are full. I have good collection of movies , games,softwares, documentaries and have some personal imp documents too........ If anyone know the real solution...please reply
March 11, 2013 7:17 AM
Quite a helpful piece of information. But still I want to ask - should I be worried about such a situation?
March 11, 2013 1:19 PM
@Peter
It's nothing to be worried about.
March 13, 2013 9:52 PM
I have a 1.5TB HDD. Total used space of every files and folders on the drive is 1.1TB. When do a properties check, it showed used 1.4TB.
That's 300GB lost, and I'm crazy to look for it even in windows or linux and no luck has come to me yet.
This article is good but still not good enough. You have to quantity each problem. For example, with a NTFS files system for a 1TB HDD, how much space would it take? etc..