In the 19th century Gregor Mendel defined the laws of genetic inheritance by crossing different types of peas. From these results arose his principle of equivalence: the gene will have the same behaviour whether it is inherited from the mother or the father. Today, several key exceptions to this principle are known, for example sex-linked traits and genes in the mitochondrial genome, whose inheritance patterns are referred to as 'non mendelian'. A third, important exception in mammals is that of genomic imprinting, where transcripts are expressed in a monoallelic fashion from only the maternal or the paternal chromosome. In this chapter, we discuss how parent-of-origin effects and genomic imprinting may play a role in autoimmunity and speculate how imprinted miRNAs may influence the expression of many target autoimmune associated genes.