<hibernate-mapping xmlns="urn:nhibernate-mapping-2.2">
   <class name="Entities.BusinessRegisterCompany, Entities" table="BusinessRegisterCompanies">
      <id name="ID" column="CompanyID" type="int" unsaved-value="0">
         <generator class="identity" />
      </id>
    <bag name="Groups" lazy="false" table="BusinessRegisterCompaniesGroups">
      <key column="CompanyID"/>
      <many-to-many class="Entities.BusinessRegisterGroup, Entities" column="GroupID"/>
    </bag>
   </class>
</hibernate-mapping>

string groups = "123,abc";
ICriteria criteria = NHibernateHelper.GetCurrentSession().CreateCriteria(typeof(T));
ICriterion[] cri = new ICriterion[1];
cri.SetValue(Expression.In("Groups", groups.Split(',')), 0);
criteria.Add(cri);
return criteria.List<T>();