Nikto is a powerful assessment tools for finding vulnerabilities in web servers.

Scanning a host
Nikto -h <Hostname/IP>

Scanning specific ports
Nikto -h <Hostname/IP> -port <Port Number>,<Port Number>

Maximum scan time
Nikto -h <Hostname/IP> -maxtime <Number in Seconds>

Scanning duration
Nikto -h <Hostname/IP> -until

Disable SSL
Nikto -h <Hostname/IP> -nossl

Force SSL
Nikto -h <Hostname/IP> -ssl

Disable 404 guessing
Nikto -h <Hostname/IP> -no404

Ignore negative responses. 302,301
Nikto -h <Hostname/IP> -IgnoreCode <Code Number>

Update the plugins and databases
Nikto -update

Specify host header
Nikto -h <Hostname/IP> -vhost

Output results
Nikto -h  <Hostname/IP> -output <filename>

Scanning through a proxy
Nikto -h <Hostname/IP> -useproxy <Proxy IP>

Host authentication
Nikto -h <Hostname/IP> -id <id:pass> or <id:pass:realm>

Database check
Nikto -h <Hostname/IP> -dbcheck

Config file
Nikto -h <Hostname/IP> -config <nikto.conf>

Disable name lookups on IP addresses
Nikto -h <Hostname/IP> -nolookup

Disable response cache
Nikto -h <Hostname/IP> -nocache

Disable interactive features
Nikto -h <Hostname/IP> -nointeractive

Display options

Nikto -h <Hostname/IP> -Display <Option>
1 Show redirects
2 Show Cookies
3 Show 200/OK responses
4 Show URL requiring authentication
D Show debug output
E HTTP Errors
P Print progress to STDOUT
S Scrub output of IP and Hostname
V Verbose output

Evasion Options

Nikto -h <Hostname/IP> -evasion <Option>
1 Random URI Encoding
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 Used windows directory separator \
A Use a carriage return (0x0d) as a request spacer
B  Use binary value (0x0b) as a request spacer

Output File Format

Nikto -h <Hostname/IP> -Format <Option>
csv       Comma-separated-value
htm    HTML Format
msf+  Log to Metaspoloit
nbe     Nessus NBE
txt       Plain text
xml    XML Format

Tuning

Nikto -h <Hostname/IP> -Tuning <Option>
1   Interesting file
2   Misconfiguration
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 Option

Mutate

Nikto -h <Hostname/IP> -mutate <Option>
1   Test all files in root directory
2   Guess for password file names
3   Enumerate user names via apache
4   Enumerate user names via cgiwrap
5   Attempt to brute force sub-domain names
6   Attempt to guess directory names from a file.