I spent waaaay too much time figuring out this one and the web is full of half-answers to this problem.

To configure a Tomcat 5.5 server realm to work with Active Directory you can crib from the following setup.

Make the following changes to the %CATALINA_HOME%/conf/server.xml file.

<Realm className="org.apache.catalina.realm.JNDIRealm" debug="0"
connectionURL="ldap://<AD SERVER ONE HOST NAME:PORT>"
alternateURL="ldap://<AD SERVER TWO HOST NAME:PORT>"
connectionName="<"DOMAIN"\"USER NAME TO BIND TO AD">" <!-- e.g. internal\serviceacct -->
connectionPassword="<YOUR PASSWORD FOR THE ABOVE ACCOUNT>"
userBase="<DN TO YOUR USERS IN AD>" <!-- e.g. OU=Users, dc=foo, dc=baz -->
userSearch="sAMAccountName={0}"
userSubtree="true"
roleBase="<DN TO YOUR GROUPS IN AD>" <!-- e.g. OU=Groups, dc=foo, dc=baz -->
roleName="CN"
roleSearch="member={0}"
roleSubtree="true"
/>


Then make the required security changes to your web.xml file for your application and you will be able to authenticate against your AD installation.