Autoimmunstoffer produceres ligeledes ofte mod selve den intrinsiske faktor; heraf gør nogle den ude al' stand til at binde vitamin B12, mens andre antistofler, mere sjældent, tillader binding af vitamin B12, men hindrer kompleksets optagelse i ileum '. Disse tre autoimmunsygdomme kaldes perniciøs anæmi (PA).
Autoantibodies are also frequently produced against intrinsic factor itself, some of which render it incapable of binding vitamin B12, with more rarely other antibodies permitting binding of vitamin B12but preventing uptake of the complex by the ileum '.