Fibromyalgia (FM) is a chronic pain syndrome characterized by widespread musculoskeletal pain and tender points. It probably results from an altered pain perception due to aberrant pain modulation system. Despite extensive research, the pathogenesis and etiology of fibromyalgia is poorly understood. It is not a primarily a muscle disorder and other systems such as neuro-endocrine, central and autonomic nervous systems have been implicated in its causation. The aim of the present study is to investigate the effect of chronic exposure to low frequency transcranial magnetic stimulation (rTMS) given at right dorsolateral prefrontal cortex on pain and its modulation status in fibromyalgia patients utilizing both subjective (standard questionnaires and psychophysical methods) and objective (nociceptive flexion reflex, diffuse noxious inhibitory controls, endogenous opioid status) and find out whether any genetic link between COMT and 5HT2A receptor genes with chroinc pain in Fibromylagia patients. The study was approved by institutional Ethical review Committee prior to commencement of the experiment. All the ethical guidelines are followed required for the human study. All subjects were explained the experimental design and written consent was taken from all the subjects. Genetic polymorphism of COMT and 5HT2A receptor genes were studied in normal controls(n=79) and fibromyalgia (n=86). Female fibromyalgia patients were recruited according to American College of Rheumatology criteria 2010. They were randomly divided into Sham (n=36) and rTMS (n=49) groups. Real rTMS (1200 pulses at 0.5 Hz per day for 5 days per week for 4 week) and sham rTMS were given rTMS and Sham groups respectively. Pain and associated symptoms were recorded by subjective (visual analogue scale and McGill pain questionnaire for pain, Spielberger State-Trait Anxiety Inventory for anxiety, Beck Depression Inventory-II for depression, WHO quality of life BREF questionnaire for quality of life, Pain coping strategy questionnaire for coping strategy and Pain belief questionnaire for general beliefs) and objective methods (nociceptive flexion reflex). Pain modulation status was assessed by diffuse noxious inhibitory controls and indirect measurement of endogenous opioids in both the groups at pre-stimulation and 2, 6, 13 and 26 weeks post-stimulation follow up periods. To associate whether any link between chronic pain with COMT and 5HT2A receptor genes, single nucleotide polymorphism study was done in fibromyalgia and normal controls. In our study, no association was observed between 5HT2A and COMT genes in FM patients. Significant reduction in pain and associated symptoms were observed from the beginning of week. Pain reduction preceded antidepressant effects. The beneficial effect of rTMS was sustained indicating a clinical application of rTMS.