Registry Run Keys / Startup Folder
Adding an entry to the "run keys" in the Registry or startup folder will cause the program referenced to be executed when a user logs in.  These programs will be executed under the context of the user and will have the account's associated permissions level.
The following run keys are created by default on Windows systems:
HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnceEx is also available but is not created by default on Windows Vista and newer. Registry run key entries can reference programs directly or list them as a dependency.  For example, it is possible to load a DLL at logon using a "Depend" key with RunOnceEx:
reg add HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\RunOnceEx\0001\Depend /v 1 /d "C:\temp\evil[.]dll" 
The following Registry keys can be used to set startup folder items for persistence:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders
HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Explorer\User Shell Folders
Adversaries can use these configuration locations to execute malware, such as remote access tools, to maintain persistence through system reboots. Adversaries may also use Masquerading to make the Registry entries look as if they are associated with legitimate programs.
BBSRAT has been loaded through DLL side-loading of a legitimate Citrix executable that is set to persist through the Registry Run key location
CORESHELL has established persistence by creating autostart extensibility point (ASEP) Registry entries in the Run key and other Registry keys, as well as by creating shortcuts in the Internet Explorer Quick Start folder.
One persistence mechanism used by CozyCar is to set itself to be executed at system startup by adding a Registry value under one of the following Registry keys:
CrossRAT uses run keys for persistence on Windows
If establishing persistence by installation as a new service fails, one variant of Elise establishes persistence for the created .exe file by setting the following Registry key:
HTTPBrowser has established persistence by setting the
S-Type may create a .lnk file to itself that is saved in the Start menu folder. It may also create the Registry key
Most Sakula samples maintain persistence by setting the Registry Run key
To establish persistence, SslMM identifies the Start Menu Startup directory and drops a link to its own executable disguised as an "Office Start," "Yahoo Talk," "MSN Gaming Z0ne," or "MSN Talk" shortcut.
Identify and block potentially malicious software that may be executed through run key or startup folder persistence using whitelisting  tools like AppLocker   or Software Restriction Policies  where appropriate. 
Monitor Registry for changes to run keys that do not correlate with known software, patch cycles, etc. Monitor the start folder for additions or changes. Tools such as Sysinternals Autoruns may also be used to detect system changes that could be attempts at persistence, including listing the run keys' Registry locations and startup folders.  Suspicious program execution as startup programs may show up as outlier processes that have not been seen before when compared against historical data.
Changes to these locations typically happen under normal conditions when legitimate software is installed. To increase confidence of malicious activity, data and events should not be viewed in isolation, but as part of a chain of behavior that could lead to other activities, such as network connections made for Command and Control, learning details about the environment through Discovery, and Lateral Movement.
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