Background: Multiple sclerosis (MS) is an acquired demyelinating disease of the central nervous system presumed to be of autoimmune nature. This MRI based study was done to see iron deposition in deep subcortical nuclei and look for any abnormalities in extracranial venous drainage system and to look for any correlation with clinical parameters . Material and Methods: This case control study was done in a single large north Indian institute and had two groups of 25 cases each. One group being of consecutive MS patients and another of other neurological disease (OND). The two groups were age and sex matched. Both the groups underwent Magnetic Resonance Venography (MRV) of neck vessels and azygous system and cross sectional areas of internal jugular veins, azygous veins were measured. Iron stores in deep grey matter nuclei were quantified with Susceptibility weighted Imaging (SWI) studies. Results: The predefined cross sectional areas of internal jugular veins ( IJV) and azygous veins were comparable. On comparing the flows of right and left IJVs, there was a clear dominance of right side in both MS and OND groups. We found more iron in all the nuclei in MS group compared to OND group. But statistically significant difference between the two groups was seen in bilateral pulvinar thalami and red nuclei, right putamen, right caudate nucleus and left substantia nigra. The absence of any difference in anatomical parameters in two groups goes against any vascular hypothesis of iron deposition in deep subcortical nuclei. The iron deposition may be an epiphenomenon of underlying disease rather than having to do something with etiopathogenesis.