Hibernate version: 3.1beta1
Annotations version: 3.1beta4
Name and version of the database you are using: MySQL 5.0.11

I defined Named Queries which are found and loaded when I'm using AnnotationConfiguration and the method addAnnotatedClass. However,
when declaring the persistent classes in hibernate.cfg.xml I get a runtime error when a Named Query is invoked.

Stack trace of the exception that occurs:

javax.servlet.ServletException: Named query not known: kunde.byNachname
org.apache.struts.action.RequestProcessor.processException(RequestProcessor.java:523)
org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:421)
org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:224)
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1194)
org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:432)
javax.servlet.http.HttpServlet.service(HttpServlet.java:709)
javax.servlet.http.HttpServlet.service(HttpServlet.java:802)

Hum, this is very weird. How are you declaring the class in the config file?

This is my hibernate.cfg.xml

<?xml version="1.0" ?>
<!DOCTYPE hibernate-configuration PUBLIC
"-//Hibernate/Hibernate Configuration DTD//EN"
"http://hibernate.sourceforge.net/hibernate-configuration-3.0.dtd">

<hibernate-configuration>
<session-factory>
<mapping class="de.hska.kundenverwaltung.db.KundeData"/>
<mapping class="de.hska.bestellwesen.db.BestellungData"/>
</session-factory>
</hibernate-configuration>

I also tried (same exception):
<hibernate-configuration>
<session-factory>
<mapping package="de.hska.kundenverwaltung.db">
<mapping package="de.hska.bestellwesen.db">

<mapping class="de.hska.kundenverwaltung.db.KundeData"/>
<mapping class="de.hska.bestellwesen.db.BestellungData"/>
</session-factory>
</hibernate-configuration>

If you can provide a simple junit runnable testcase that reproduce the issue, then, post it to JIRA.

The problem is the annotations documentation.

In chapter 1.2 there is:
"sessionFactory = new AnnotationConfiguration().
.add...
.buildSessionFactory();"

When you are using hibernate.cfg.xml then you have to invoke the method configure() for the created AnnotationConfiguration object. Same procedure as using Hibernate w/o annotations.