A major logical section of the registry. Subtrees are the root keys of the registry, and all other registry keys are subkeys of these root keys. The following table summarizes the functions of the five subtrees of the Microsoft Windows NT and Windows 2000 registries.
| Subtree | Function |
| HKEY_LOCAL_MACHINE | Contains configuration information for the local machine, including all hardware and software settings |
| HKEY_CLASSES_ROOT | Provides compatibility with Windows 3. x and points to the Classes subkey of HKEY_LOCAL_MACHINE |
| HKEY_CURRENT_CONFIG | Provides information about the active hardware profile |
| HKEY_CURRENT_USER | Contains the settings of the user who is currently logged on interactively and points to the SID_# of HKEY_USERS, in which SID_# is the security ID string of the current user |
| HKEY_USERS | Contains default system settings and the settings of the user who is currently logged on interactively, plus all previously logged on users |
In Microsoft Windows 95 and Windows 98, a sixth subtree called HKEY_DYN_DATA is generated dynamically and is used for performance measuring via System Monitor and plug and play configuration of devices. This subtree is also called the hardware tree.
Most Windows NT and Windows 2000 registry troubleshooting takes place in the HKEY_LOCAL_MACHINE\System\CurrentControlSet subkey.