Rheumatoid arthritis (RA) is an autoimmune/inflammatory disorder with a complex geneticcomponent. RA is characterized by chronic inflammation of the synovial membrane in the joint,which leads to the progressive destruction of articular cartilage, ligament and bone. Severalcytokines such as tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6)have been implicated in the pathological mechanisms of synovial tissue proliferation, jointdestruction and programmed cell death in rheumatoid joint. Genome wide screening of subjectssuffering from autoimmune diseases especially arthritis revealed linkage to inflammatorymolecules like TNF-α, IL-1β and IL-6, inducible nitric oxide synthase (iNOS), cyclooxygenase-2(COX-2 ), nuclear factor-kappaB (NF-κB) and human leucocyte antigen/major histocompatibilitycomplex (HLA/MHC) locus. The status of the pharmacological mechanism of herbal drugs in thelight of genome wide screening results has been discussed to reinforce the therapeutic potentialand the pharmacological basis of the herbal drugs.