What is the best way to describe a ManyToMany relationship in hibernate.
i have User and Document objects.
depending on what access a user has, the user can access various different documents.
and a document can be accessed by various different users.

so should I create a third object UserDocument Object OR use @JoinTable for the Many to Many Relationship.
In either case how will Hibernate behave in terms of returning the objects.

Hibernate will create a MTM table for you.
You just need to specify the @JoinTable annotation where you can set the MTM table name


In case you do not specify the name the default will be used

Thanks for the answer. So is @JoinTablethe best way to describe a MTM?
When Hibernate returns the objects how will the MTM be represented and how would I access the values?

You don't have to carry about MTM object. Hibernate does it.
Just make your query for the given object - myEntity.getItems() and you'll get your list

Cool. Thanks. Will this still work if I use annotation based mapping and SQL scripts to create my Database.
What changes should I make to the tables participating in the join?

eg:
User and Document Tables
User ( id, username )
Document (id, documentName)

How will Hibernate create the Join Table? Will it create the Join Table on every deploy?
I wouldn't want hibernate to create a Join Table (through Hibernate). Instead would prefer to create the Join table using SQL script.

As I can understand you need it to put some additional info.
This you can achieve by creating a third object that will represent your MTM table.
So it will look like this:
user --> users_documents <-- document
That means create OTM relations from user and document to users_documents

Looks a bit complicated.
How should I change the @JoinTable annotation to use the Third Object?

@JoinTable create a third table, but it tells hibernate to manage it (using primary keys)
Anyway, which data (columns) do you want to hold in your users_documents table?