Summary: 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.
Related:
Ask Leo! - How can I tell what's taking up so much disk space?
Ask Leo! - Why isn't there 80 gigabytes of free space on my empty 80 gigabyte drive?
Ask Leo! - Can I adjust some master NTFS table size to handle large number of files better?
Article C3122 - August 19, 2007
I have exactly the same scenario. I downloaded a program called HDGraph from SourceForge to analyse the disk space. THe program says that it cant read 40G of data due to permission issues/bad sectors adn what not. I have tried posting it to Vista forums as well with no replies. Plz help
Posted by: Matrix at November 7, 2008 7:06 PMA lot of space can be cleared by turning off system restore in control panel
Posted by: Poo at November 7, 2008 8:10 PMTo say it better,System Restore Points are calculated in size when you right click your drive and see the properties,but when you go into the drive and select all and right click and see properties they are not added to the total size you see there.My 60gb HDD had a 8gb difference, turning off System Restore fixed the discrepancy.
Posted by: Poo at November 8, 2008 7:54 AMBut you also lose the benefits of system restore.
yes i have same problem with my hard drive seagate 1tb it start to decrease incrementally every day then it stopped at 599. i think if i did not laugh my head of insanely, every time i saw the gb's go down [lol thought of marry poppins then] my pc would be quite cripple by now. It is now showing 399 used space with 531 free space [i recently added all the star trek next gen episodes {this explains the change from 599 to 531}]
Posted by: tiove at December 20, 2008 5:51 PMPlease help me my email is [personal email address removed].
AHOI!!!! ok so i turned off the 'hide protected operating system files [recommended]' and my used space went up from 170gb to 260 [this is opening c drive, selecting all folders and as you know right click properties] but still i had 399 used space in the actual properties of the c drive in my computer, anyway thanks to the user: Poo i turned off my system restore and WHAM free space 670 and used 260 bada boom! very happy but i have rechecked my system restore...aww common its *in gollums slimy voice* 'too risky.. too risky!!!' well yeah so if i see an incremental drop in free space i know what its about now, so thanks a lot
Posted by: tiove at December 20, 2008 6:08 PMhello i am having the same problem on my new laptop i intalled some updates and the coputer was telling me that i had used 50g of space how can i fix this i dont want my hard drive filled up thx
Posted by: tom finch at December 29, 2008 1:08 PMI am using a Lenovo T60 laptop and it has 60gb hard disk in it. The avalable harddisk space 55gb. I used to delete the unanted temporary files, temporary internet files, cookies, prefetch, etc to maintain good performance of the PC. And there was 20gb free space which one day gradually decreased to 3gb,1gb,712mb,400mb,100mb and even worse to KB of 156kb and finally to 0bytes of free hard disk space and pops up disk cleanup utility to clean up hard disk. So i am unable to run any programs or work on it properly. Even if i free up unwanted files as well as wanted data and free up space in it, the free space decreases immediately to 66mb or lesser free space which makes the PC slow. I have not installed any unwanted programs other than the usual wanted softwares an i am pretty sure about that. I suspect if this is a virus or spyware issue.
13-Jan-2009
Is there anyway to make System Restore use less space if we would like to have the benefit of a restore, but not use up all our space? I just saved half my hard drive by taking System Restore off.
Thanks for that, by the way.
23-Jan-2009
in my computer the c drive size become less every day about 1 mb decrease in size of my 9.31gb hard disk, so what is the solution?
Posted by: khan at March 21, 2009 8:07 AMin explorer go to tools, folder options, view. then, make sure to mark "display system folders". you will see a "recycler" folder directly under C-drive. a lot of deleted items are stored there for some reason. so you have to extra delete your files.
Posted by: eindig at May 1, 2009 5:09 AM