Two clinical trials of SARS CoV-2 adenovirus vector -based vaccines have been temporarily halted due to autoimmune complications concerns in some participants. Similarly, SARS CoV-2 RNA vaccines possess a theoretical potential to elicit autoimmune complications. After their approval to combat the current COVID-19 pandemic, nucleic acid-based vaccination, whether DNA or RNA, is considered first of its kind to be used in humans. Potential risks including development of autoimmune diseases might only be documented when used on a large scale as the clinical trials have involved only tens of thousands of participants. Thus, a strict system for post marketing surveillance must be secured to report any potential adverse effect and the techniques used in development of these types of vaccines should focus on innovative methods to decrease their potential autoimmunity. Importantly, smokers, obese and diabetic participants are more liable groups to develop autoimmune diseases and we recommend a personalized risk benefit ratio to be evaluated before vaccination waiting for further safety data coming from post marketing surveillance. Finally, quitting smoking, loss of overweight and control of blood glucose levels might help to lower their probabilities in case of the benefits exceeded the risks.