Nikto is not designed as a stealthy tool. It will test a web server in the quickest time possible and is obvious in log files or to an IPS/IDS. However, there is support for LibWhisker’s anti-IDS methods in case you want to give it a try (or test your IDS system).

Not every check is a security problem, though most are. There are some items that are “info only” type checks that look for things that may not have a security flaw, but the webmaster or security engineer may not know are present on the server. These items are usually marked appropriately in the information printed. There are also some checks for unknown items which have been seen scanned for in log files.

  
Options:
-ask+               Whether to ask about submitting updates
                      yes   Ask about each (default)
                      no    Don't ask, don't send
                      auto  Don't ask, just send
-Cgidirs+           Scan these CGI dirs: "none", "all", or values like "/cgi/ /cgi-a/"
-config+            Use this config file
-Display+           Turn on/off display outputs:
                        1     Show redirects
                        2     Show cookies received
                        3     Show all 200/OK responses
                        4     Show URLs which require authentication
                        D     Debug output
                        E     Display all HTTP errors
                        P     Print progress to STDOUT
                        S     Scrub output of IPs and hostnames
                        V     Verbose output
-dbcheck           Check database and other key files for syntax errors
-evasion+          Encoding technique:
                        1     Random URI encoding (non-UTF8)
                        2     Directory self-reference (/./)
                        3     Premature URL ending
                        4     Prepend long random string
                        5     Fake parameter
                        6     TAB as request spacer
                        7     Change the case of the URL
                        8     Use Windows directory separator (\)
                        A     Use a carriage return (0x0d) as a request spacer
                        B     Use binary value 0x0b as a request spacer
-Format+           Save file (-o) format:
                        csv   Comma-separated-value
                        htm   HTML Format
                        msf+  Log to Metasploit
                        nbe   Nessus NBE format
                        txt   Plain text
                        xml   XML Format
(if not specified the format will be taken from the file extension passed to -output)
-Help              Extended help information
-host+             Target host
-IgnoreCode        Ignore Codes--treat as negative responses
-id+               Host authentication to use, format is id:pass or id:pass:realm
-key+              Client certificate key file
-list-plugins      List all available plugins, perform no testing
-maxtime+          Maximum testing time per host
-mutate+           Guess additional file names:
                        1     Test all files with all root directories
                        2     Guess for password file names
                        3     Enumerate user names via Apache (/~user 
                              type requests)
                        4     Enumerate user names via cgiwrap 
                              (/cgi-bin/cgiwrap/~user type requests)
                        5     Attempt to brute force sub-domain names, 
                              assume that the host name is the parent domain
                        6     Attempt to guess directory names from the 
                              supplied dictionary file
-mutate-options    Provide information for mutates
-nointeractive     Disables interactive features
-nolookup          Disables DNS lookups
-nossl             Disables the use of SSL
-no404             Disables nikto attempting to guess a 404 page
-output+           Write output to this file ('.' for auto-name)
-Pause+            Pause between tests (seconds, integer or float)
-Plugins+          List of plugins to run (default: ALL)
-port+             Port to use (default 80)
-RSAcert+          Client certificate file
-root+             Prepend root value to all requests, format is /directory
-Save              Save positive responses to this directory ('.' for auto-name)
-ssl               Force ssl mode on port
-Tuning+           Scan tuning:
                        1     Interesting File / Seen in logs
                        2     Misconfiguration / Default File
                        3     Information Disclosure
                        4     Injection (XSS/Script/HTML)
                        5     Remote File Retrieval - Inside Web Root
                        6     Denial of Service
                        7     Remote File Retrieval - Server Wide
                        8     Command Execution / Remote Shell
                        9     SQL Injection
                        0     File Upload
                        a     Authentication Bypass
                        b     Software Identification
                        c     Remote Source Inclusion
                        x     Reverse Tuning Options 
                              (i.e., include all except specified)
-timeout+          Timeout for requests (default 10 seconds)
-Userdbs           Load only user databases, not the standard databases
                   all   Disable standard dbs and load only user dbs
                   tests Disable only db_tests and load udb_tests
-until             Run until the specified time or duration
-update            Update databases and plugins from CIRT.net
-useproxy          Use the proxy defined in nikto.conf
-Version           Print plugin and database versions
-vhost+            Virtual host (for Host header)
       + requires a value