COVID–19 and Autoimmune disease are present in a patient simultaneously can ruin life because of two reasons chiefly. Firstly diagnosed patient receiving immunosuppressant therapy is simply vulnerable to COVID–19 which generally attacks the immune system. Secondly, those huge undiagnosed symptomatic cases can have the risk of the overactive immune system leading to a Cytokine storm. We look into the molecular basis of both COVID–19 and autoimmune diseases with drugs acting upon them to find out the answer to the questions arising out of the diagnosis and treatment of these cases. It is the ACEII type receptors which are the first contact points of COVID –19 ultimately resulting in the huge proliferation of pro–inflammatory cytokines leading to cytokine storm. Autoimmunity also involves the down regulation of regulatory T–cells and up regulation of T effector cells leading huge cytokine release as comparable to cytokine storm. Then Mechanisms of relevant drugs were studied. We concluded after reviewing the different literature that on the molecular basis of these two groups of diseases screening tests should be suggested to all of the symptomatic cases immediately for both autoimmunity and COVID–19 infected patients and use of rationale drug therapy keeping eye on immunosuppression and cytokine over activity