Pernicious anaemia is the most common cause of vitamin B12 deficiency. It is an AUTOIMMUNE condition that affects your stomach. A protein called intrinsic factor attaches itself to vitamin B12 in your stomach, so it can be absorbed from food you eat. Pernicious anaemia causes your immune system to attack the cells in your stomach that produce the intrinsic factor. This means your body cannot absorb vitamin B12 which causes a deficiency.