White space is significant in XML and therefore in JDOM.
import org.jdom.*;
import org.jdom.output.XMLOutputter;
import java.io.IOException;
public class PrettyHelloJDOM {
  public static void main(String[] args) {
   
    Element root = new Element("GREETING");
    	
    root.setText("\n  Hello JDOM!\n");
         
    Document doc = new Document(root);      
    
    // At this point the document only exists in memory.
    // We still need to serialize it
    XMLOutputter outputter = new XMLOutputter();
    try {
      outputter.output(doc, System.out);       
    }
    catch (IOException e) {
      System.err.println(e);
    }
  }
}
If white space is not significant in your application, you can instruct the outputter to clean it up for you.