Attackers could execute unauthorized commands, which could then be used to disable the software, or read and modify data for which the attacker does not have permissions to access directly. Since the targeted application is directly executing the commands instead of the attacker, any malicious activities may appear to come from the application or the application's owner.

If at all possible, use library calls rather than external processes to recreate the desired functionality.

Run your code in a "jail" or similar sandbox environment that enforces strict boundaries between the process and the operating system. This may effectively restrict which commands can be executed by your software.

Examples include the Unix chroot jail and AppArmor. In general, managed code may provide some protection.

This may not be a feasible solution, and it only limits the impact to the operating system; the rest of your application may still be subject to compromise.

Be careful to avoid CWE-243 and other weaknesses related to jails.

For any data that will be used to generate a command to be executed, keep as much of that data out of external control as possible. For example, in web applications, this may require storing the command locally in the session's state instead of sending it out to the client in a hidden form field.

Use languages, libraries, or frameworks that make it easier to generate properly encoded output.

Examples include the ESAPI Encoding control.

Properly quote arguments and escape any special characters within those arguments. If some special characters are still needed, wrap the arguments in quotes, and escape all other characters that do not pass a strict whitelist. Be careful of argument injection (CWE-88).

If the program to be executed allows arguments to be specified within an input file or from standard input, then consider using that mode to pass arguments instead of the command line.

If available, use structured mechanisms that automatically enforce the separation between data and code. These mechanisms may be able to provide the relevant quoting, encoding, and validation automatically, instead of relying on the developer to provide this capability at every point where output is generated.

Some languages offer multiple functions that can be used to invoke commands. Where possible, identify any function that invokes a command shell using a single string, and replace it with a function that requires individual arguments. These functions typically perform appropriate quoting and filtering of arguments. For example, in C, the system() function accepts a string that contains the entire command to be executed, whereas execl(), execve(), and others require an array of strings, one for each argument. In Windows, CreateProcess() only accepts one command at a time. In Perl, if system() is provided with an array of arguments, then it will quote each of the arguments.

Assume all input is malicious. Use an "accept known good" input validation strategy (i.e., use a whitelist). Reject any input that does not strictly conform to specifications, or transform it into something that does. Use a blacklist to reject any unexpected inputs and detect potential attacks.

Use a standard input validation mechanism to validate all input for length, type, syntax, and business rules before accepting the input for further processing. As an example of business rule logic, "boat" may be syntactically valid because it only contains alphanumeric characters, but it is not valid if you are expecting colors such as "red" or "blue."

When constructing OS command strings, use stringent whitelists that limit the character set based on the expected value of the parameter in the request. This will indirectly limit the scope of an attack, but this technique is less important than proper output encoding and escaping.

Note that proper output encoding, escaping, and quoting is the most effective solution for preventing OS command injection, although input validation may provide some defense-in-depth. This is because it effectively limits what will appear in output. Input validation will not always prevent OS command injection, especially if you are required to support free-form text fields that could contain arbitrary characters. For example, when invoking a mail program, you might need to allow the subject field to contain otherwise-dangerous inputs like ";" and ">" characters, which would need to be escaped or otherwise handled. In this case, stripping the character might reduce the risk of OS command injection, but it would produce incorrect behavior because the subject field would not be recorded as the user intended. This might seem to be a minor inconvenience, but it could be more important when the program relies on well-structured subject lines in order to pass messages to other components.

Even if you make a mistake in your validation (such as forgetting one out of 100 input fields), appropriate encoding is still likely to protect you from injection-based attacks. As long as it is not done in isolation, input validation is still a useful technique, since it may significantly reduce your attack surface, allow you to detect some attacks, and provide other security benefits that proper encoding does not address.

Use automated static analysis tools that target this type of weakness. Many modern techniques use data flow analysis to minimize the number of false positives. This is not a perfect solution, since 100% accuracy and coverage are not feasible.

Use dynamic tools and techniques that interact with the software using large test suites with many diverse inputs, such as fuzz testing (fuzzing), robustness testing, and fault injection. The software's operation may slow down, but it should not become unstable, crash, or generate incorrect results.

Run the code in an environment that performs automatic taint propagation and prevents any command execution that uses tainted variables, such as Perl's "-T" switch. This will force you to perform validation steps that remove the taint, although you must be careful to correctly validate your inputs so that you do not accidentally mark dangerous inputs as untainted (see CWE-183 and CWE-184).

Use runtime policy enforcement to create a whitelist of allowable commands, then prevent use of any command that does not appear in the whitelist. Technologies such as AppArmor are available to do this.

Assign permissions to the software system that prevent the user from accessing/opening privileged files. Run the application with the lowest privileges possible (CWE-250).