Hi Ghamdinh,
The flags are used in clinical assessment to indicate possible serious underlying pathology (for red flags) and psychosocial issues (for yellow flags). The following link http://student.bmj.com/issues/03/04/education/97.php gives a brief summary on the bmj's student page.
However this list is not exhaustive, as there are now orange (severe psychological), blue (socioeconomic) and black flags (occupation)!! The following link gives a very brief explanation www.rcplondon.ac.uk/pubs/clinicalmedicine/0206novdec/0206_nov_conf1.htm if you go to the "psychosocial barriers to recovery" section. I think red and yellow are still most commonly used in clinical, with the other flags being relatively new.
Hope this was of use,
Rachie