Think about this simple database schema:

 User                Course              StudentCourse       Student
+-------------+     +-------------+     +-------------+     +-------------+
| -user_id    |1   *| -course_id  |1   *| -course_id  |*   1| -student_id |
|             |---->| -user_id    |---->| -student_id |---->|             |
+-------------+     +-------------+     +-------------+     +-------------+

[1   *] = 1 to many relationship 

I've produced organizations for that User, Course, and Student objects, and hang in the following mappings:

User   -> Course  - one to many
Course -> Student - many to many

During my Java classes I'm able to access the Courses of the User by calling user.getCourses() and that i can access all of the Students inside a Course by calling course.getStudents(). I wish to have the ability to find all the Students in most from the Courses trained with a specific User like user.getCourse().getStudents(), but because user.getCourses() returns Collection<Course> I am unable to call course.getStudents() around the Collection. How must i implement this with Hibernate? Is really a named query my only option?

i suppose you need to define fetchType = EAGER in Course, that is really not recommended so HQL might be best and efficient.

You could do this the next:

List<Student> students = new ArrayList<Student>();
for ( Course course : user.getCourses() )
{
    students.addAll( course.getStudents() );
}

However this is very inefficient (begin to see the "SELECT N+1" problem)

I've not had an opportunity to test drive it however your named query must be something similar to: "Choose c.students FROM Course c WHERE c.user.title = 'username'"

You stated

I wish to have the ability to find all the Students in most from the Courses trained with a specific User

Use HQL query

SELECT DISTINCT _student FROM User AS _user, IN ( _user.courses ) _course, IN( _course.students ) _student WHERE _user.id = :id

or

SELECT DISTINCT _student FROM User _user inner join _user.courses _course inner join _course.students _student WHERE _user.id = :id

regards,