You need to specify a value for each one.
For instance:
<cfinput type="checkbox" name="gender" value="Male" checked>
</label></td>
<td>Female</td>
<td><label>
<cfinput type="checkbox" name="gender" value="Female">
</label></td>
When you process the page, the Form.Gender variable will contain either "Male" or "Female" depending on which is checked (or "Male,Female" if both are checked, which can be used as a list incidentally). Make sure to use
<cfif IsDefined("Form.Gender")> before checking for the values, otherwise it will throw an error if none of the checkboxes are checked, unless you've created it with <cfparam>.
<cfparam name="Form.Gender" default="">
<cfif Form.Gender EQ "Male">
<!--- Do something --->
<cfelseif Form.Gender EQ "Female">
<!--- Do something else --->
</cfif>
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since Feb 2008