how could I pass parameters to a stored procedure in the hibernate mapping file from Java code.

First of all :Hibernate numbers parameters from zero contrary to JDBC

About your question:

This goes in the mapping file:

<query name="eg.DomesticCat.by.name.and.minimum.weight">< ![CDATA[
    from eg.DomesticCat as cat
        where cat.name = ?
        and cat.weight > ?
] ]></query>

Parameter binding and executing is done programatically:

Query q = sess.getNamedQuery("eg.DomesticCat.by.name.and.min imum.weight");
q.setString(0, name);
q.setInt(1, minWeight);
List cats = q.list();

The fact that the parameter are indexed from zero can be effectively ignored by using named parameters, like so...

<query name="eg.DomesticCat.by.name.and.minimum.weight">< ![CDATA[
    from eg.DomesticCat as cat
        where cat.name = :name
        and cat.weight > :weight
] ]></query>

Query q = sess.getNamedQuery("eg.DomesticCat.by.name.and.min imum.weight");
q.setString("name", name);
q.setInt("weight", minWeight);
List cats = q.list();

I'm sure that you'll agree - this is less error prone, more robust (when the query changes) and much more intuitive to read.