Molecular farming in plants or plant cell cultures represents a viable alternative technology that holds great promise for the low-cost and large-scale production of recombinant proteins. The particular case of plant-based vaccines for the prevention of autoimmune diseases is addressed here, presenting a comprehensive overview of the different molecules and expression technologies that have been investigated so far in both academia and industry. The potential of plants not only as bioreactors but also as delivery systems for pharmaceuticals is discussed, and the advantages of oral delivery of autoantigens for the induction of immune tolerance are highlighted.