Autoimmune diseases are a broad class of disorders that are characterised by the irregular response of immune cells creating self-reactive antibodies that target its own cells and tissues. The primary cause for the development of autoimmunity is yet to be known. However, current research suggests that increased genetic susceptibility combined with multitude of triggering elements such as environmental influences and infection are some of the most significant causative factors leading to autoimmunity. Using the above-mentioned factors, till date, researchers have proposed several theories in an attempt to explain the underlying mechanisms and complexities of how autoimmunity occurs. Some of the most widely accepted theories include cryptic determinants, molecular mimicry, altered glycan theory, and the hygiene hypothesis as well as the interaction of B and T lymphocytic cells. Understanding these molecular mechanisms of autoimmune diseases is key for the development of future preventative therapies, as currently there is no therapeutic strategy to cure these conditions. The traditional concept of T cell-mediated and autoantibody-mediated autoimmune diseases should be adjusted to reflect the new understanding of the interaction of different immune cells in autoimmune pathogenesis. Recognition of B cell contribution to the pathogenesis of autoimmune diseases (traditionally thought to be mediated by T cells) has led to promising new therapies.