Detecting Persistence on Windows Computers

An Guide for Non-Technical Users

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Introduction

Cyber threats continue to evolve, and one common method attackers use to maintain access to a compromised computer is known as persistence. This means that malicious software (malware) remains active even after your PC restarts, making it difficult to detect and remove.

While identifying persistence mechanisms may seem complex, it is within reach for any Windows user willing to learn a few key signs and basic investigative steps. This guide will walk you through how to recognize common indicators of persistence, including unexpected Command Prompt windows at startup, reviewing hidden startup programs in the Windows Registry, and spotting suspicious commands involving PowerShell, cmd, rundll32, and wmic.

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Common Signs That Persistence Might Be Present

Malware that uses persistence tries to stay hidden and keep running on your computer even after restarts. While it can be tricky to spot, there are some warning signs you can watch out for. These signs don’t require technical expertise and can help you identify if something suspicious might be happening on your Windows PC. Here are some of the most common clues that persistence could be active on your system.

1. Command Prompt (cmd) Windows Appearing During Startup Explanation: Legitimate startup processes usually run quietly. Seeing a Command Prompt window pop up suggests a script or command is running automatically, which could be a persistence method. How to Check:

   • Pay attention during startup. If you see the window briefly flash, try to note what command is shown (if any).
   • Open Task Manager (press Ctrl + Shift + Esc), go to the Startup tab, and look for unfamiliar entries that may be running scripts or commands.
   • If unsure, research the names of startup programs online.

2. Unusual or Unexpected Network Activity Explanation: Malware often communicates with remote servers to receive instructions or send stolen data. Unexpected network traffic can be a sign of this ongoing activity. How to Check:

   • Use Task Manager or Resource Monitor (search in the Start menu) to view network usage by process.
   • If an unknown or suspicious program is using the network heavily, that might indicate persistence.
   • Consider running a trusted antivirus or network monitoring tool for deeper inspection.

3. Sudden Decline in System Performance Explanation: Persistent malware can run background tasks that consume CPU or memory resources, slowing your system without obvious cause. How to Check:

   • Open Task Manager and check which processes are consuming the most CPU or memory.
   • If you see unknown or suspicious processes using significant resources, investigate their names online.
   • Close unnecessary startup programs to improve performance.

4. Unfamiliar Software or Applications Installed Explanation: Malware often installs additional software to maintain persistence or enable other malicious activities. How to Check:

   • Open Settings > Apps & Features or Control Panel > Programs and Features and review the list of installed programs.
   • Look for software you don’t recognize or remember installing.
   • Search the program names online to verify legitimacy.

5. Modifications to Startup Programs or System Settings Explanation: Malware frequently adds itself to startup lists or changes system configurations to run automatically and avoid removal. How to Check:

   • Open Task Manager > Startup tab to view and manage programs set to run at startup.
   • Use Registry Editor (regedit) to review startup keys (see Registry section in the guide).
   • Use tools like Autoruns (free Microsoft Sysinternals utility) to get a comprehensive list of all startup items and spot suspicious entries.

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How to Check for Persistence in the Windows Registry

The Windows Registry is a critical database that controls many system settings, including which programs automatically start when your PC boots. Because of this, attackers often target the registry to add entries that ensure malware runs persistently every time your system starts.

Manually inspecting the registry can be complex and risky, so to simplify this process, you might consider using my Registry Persistence Detector — a tool that I designed to help identify common persistence entries quickly.

Important: While this tool can greatly streamline your investigation, it does not detect every possible form of registry persistence. Additionally, the registry is a sensitive area; before deleting any entries, always back up the keys you plan to modify or remove. False positives can occur, so whenever possible, verify suspicious entries by researching them online or consulting a trusted expert before making changes.

If you prefer to check manually, here’s how:

1. Open the Registry Editor

   • Press Windows key + R to open the Run dialog.
   • Type regedit and press Enter.
   • If a security prompt appears, click Yes to continue.

2. Navigate to Common Startup Locations In the left panel, go to each of these paths one at a time:

   HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Run  
   HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\RunOnce  
   HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\Run  
   HKEY_LOCAL_MACHINE\Software\Microsoft\Windows\CurrentVersion\RunOnce  
   

3. Review Entries for Suspicious Items

   • On the right, examine the list of entries, which include program names and the file paths or commands they execute.
   • Be alert for entries with unusual or random names.
   • Pay particular attention to entries pointing to executables in unexpected locations such as Temp, AppData, or other non-standard folders.

4. Watch for Script or Command Executions Some entries may launch scripts or commands rather than standard programs. For example, an entry running:

   cmd.exe /c <command>  
   

   could be an indicator of persistence.

5. Verify Before Taking Action Many registry startup entries are legitimate and necessary. If you encounter unfamiliar entries, research their names and file paths online to determine whether they are safe or potentially malicious before deleting them.

How to Safely Back Up Registry Keys Before Making Changes

1. Open Registry Editor (regedit), and navigate to the key you want to back up.
2. Right-click the key (for example, Run or RunOnce) in the left sidebar.
3. Select Export.
4. Choose a safe location on your computer to save the backup file.
5. Give the file a descriptive name (e.g., Run_Backup_2025-07-06.reg).
6. Click Save.

This creates a .reg file you can use to restore the key if needed by double-clicking the file and confirming the import.

How to Use the Registry Persistence Detector Tool

Manually checking the Windows Registry for persistence threats can be overwhelming. The Registry Persistence Detector simplifies this task by scanning key areas in the Windows Registry where malware commonly hides startup entries.

I designed this free GUI tool to help users identify and optionally remove suspicious entries — with helpful features like PowerShell and encoded payload detection, 32/64-bit registry views, and built-in safe deletion with optional backup.

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What It Does

• Scans common registry locations where persistence is known to occur.

• Highlights suspicious entries based on:

  • Use of PowerShell or encoded payloads (e.g., base64).
  • Known suspicious keywords (like keylogger, trojan, etc.).
  • Unusual command patterns (e.g., cmd.exe, rundll32, encoded strings).

• Offers optional removal of detected entries, with a prompt to back up the registry value before deletion.

What It Does Not Do

• It cannot detect all forms of persistence. Some advanced malware uses more complex or obscure techniques not covered here.
• The tool may produce false positives — not everything flagged is malicious. Always research unfamiliar entries or consult a professional before removal.
• It does not scan non-registry persistence mechanisms like scheduled tasks, services with unusual binaries, or WMI event subscriptions.

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Running the Tool

You can run it via Python or as a pre-built executable:

Option 1: Using the Precompiled .exe

1. Download the tool from: https://github.com/kaotickj/persistenceDetector

2. Run detectpersist.exe by double-clicking it.

   • You may be prompted to run as Administrator (which is recommended for full access).

Option 2: Using Python (if you prefer source)

1. Clone the repository:

   git clone https://github.com/kaotickj/persistenceDetector.git
   cd persistenceDetector

2. Run the tool:

   python detectpersist.py

ℹ️ Python 3.7+ and Tkinter are required. Tkinter is typically included by default.

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Using the Interface – Step-by-Step

Once the application launches:

1. Select Scan Options (Top-Left)

   • ✅ Powershell Commands: Enable this to flag registry entries that launch PowerShell — often used in malware.
   • ✅ Encoded Payloads: Enable this to flag base64 or obfuscated commands — common in evasive attacks.

2. Choose Registry View (Top-Right)

   • If you're on a 64-bit system, scan both 32-bit and 64-bit views separately.

     • First scan with 32-bit selected.
     • Then switch to 64-bit and scan again.

   • On 32-bit systems, just use the default 32-bit view.

3. Click “Check Registry” The scan checks known persistence locations, including:

   • HKCU and HKLM Run/RunOnce keys
   • Internet Explorer extension keys
   • Services, HKEY_USERS, and shell handlers

4. Review the Output (Middle Panel) If any suspicious entries are found:

   • They will appear in the output panel.
   • A dropdown box at the bottom will list each entry for easy selection.

5. Deleting an Entry (Optional and Safe)

   • Select an entry from the dropdown.
   • Click "Delete Selected".
   • You’ll be asked whether to back up the entry before deletion. This is strongly recommended in case you need to restore it later.

6. Running as Administrator

   • If you're not running with admin rights, some entries (especially under HKLM) may not be visible or removable.
   • Go to Menu → Run as Administrator to elevate permissions and re-scan.

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Tips for Safe Use

• 🔍 Always back up registry entries before deletion. The tool offers a save prompt for exporting entries as .reg files.
• 🧠 Research unfamiliar entries before deleting. Some legitimate software creates registry startup entries.
• ⚠️ Use both 32-bit and 64-bit scans on 64-bit systems for full coverage.
• 🧰 Use this tool alongside antivirus and anti-malware software — it's part of a layered defense.

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Checking for Persistence via PowerShell, cmd, rundll32, and wmic

Advanced attackers often leverage legitimate Windows tools to maintain a low profile while keeping control over compromised systems. These tools—while powerful and useful for system administrators—can also be exploited for persistence. Here’s what to look for:

• PowerShell PowerShell is frequently used in modern attacks due to its flexibility and scripting capabilities. Malicious commands are often base64-encoded or obfuscated to avoid detection. If you notice PowerShell scripts set to run at startup or as scheduled tasks—and especially if the commands appear encoded or overly complex—they warrant closer inspection.

• Command Prompt (cmd) Cmd-based persistence may involve scripts or batch files triggered at login or startup. Look for cmd commands embedded in startup entries, scheduled tasks, or registry keys—particularly those invoking suspicious scripts, tools, or internet connections.

• rundll32.exe This utility executes functions from DLLs (dynamic-link libraries). While legitimate, it is often abused to load malicious code discreetly. Investigate any rundll32 commands that launch unknown DLLs or reference files in uncommon locations such as AppData, Temp, or the root of the *C:* drive.

• wmic (Windows Management Instrumentation Command-line) WMIC allows command-line access to system management functions. Although deprecated in recent Windows versions, attackers still use it in legacy environments. Be cautious of WMIC commands embedded in scripts or scheduled tasks, especially if they interact with user accounts, processes, or system startup.

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What to Do If You Suspect Persistence or Infection

Identifying potential persistence mechanisms is a strong first step—but safely removing them without damaging your system requires care. If you suspect your computer is compromised:

• Run a full system scan using trusted antivirus or anti-malware software.
• Avoid removing suspicious files or registry entries blindly. Missteps can damage your system or delete legitimate components.
• Research unfamiliar commands or filenames before taking action, and verify their legitimacy whenever possible.
• Seek assistance from a cybersecurity professional or experienced technician if you are unsure how to proceed.
• Keep Windows and all software updated to minimize known vulnerabilities that malware can exploit.

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Conclusion

You don’t need to be a cybersecurity expert to recognize signs of persistent malware on your system. With some curiosity and the right guidance, you can learn to identify unusual behavior, investigate potential threats, and take steps to protect your computer.

While tools like Registry Persistence Detector can make the process more accessible, understanding the underlying concepts—like suspicious registry entries, startup commands, and misuse of system utilities—empowers you to respond more confidently.

Stay proactive, stay informed, and don’t hesitate to ask for help. Your system security is worth protecting.