It really depends on your use case for accessing/managing these files. If you're going to be enumerating the files a lot (or portions of the files) then everything in one directory/folder may not be the best. You can at least "chunk up" the enumeration by subfolder if you create those. Also, if you break them up into subfolders in some logical way, then managing those units and/or groupings of files will become much easier. I.E. Backups, restoring, archiving, deleting. If you are storing the path to each file in a database, then you're going to get the same performance either way (subdirectories and everyone in the pool together). Can you explain a little more about the repository and how you'll be using it?