Autoimmune diseases are the third leading cause of morbidity after cardiovascular diseases and cancer in industrialised world. Genetics and environmental factors have a negative impact on immune system’s ability to distinguish self from non-self antigens mediated by autoantibodies and autoreactive T cells.The outcome rates in genetic polymorphisms account for only 20% of the phenotypic variance, among monozygotic twins are 25-40%, suggesting that non-heritable environmental factors play a more significant role. Systemic autoimmune diseases are thought to result from immune dysregulation in genetically susceptible individuals who are exposed to multifactorial environmental risk factors, along with hormonal and immune defects as well.It is difficult to establish a direct link between one particular environmental factor and development of the disease. The most widely accepted triggers that effect autoimmunity through epigenetic mechanisms are drugs, pollutants, infections and microbiome, solar radiation and vitamin D deficiency, nutrition, introduced complementary food and breastfeeding implicated in infants. Proper activation of the pattern recognition receptors of the innate immune system demonstrates a crucial role in early development of the immune system. These processes already start in utero and prenatal, as well as early postnatal developmental stages for allergy-preventing environmental influences.As for microbial components associating with our modern lifestyle, inflammatory disorders in allergic diseases are steadily increasing due to reduced exposure to them. Therefore, imbalance responsible for cellular and molecular mechanisms of autoimmune disease phenomena include altering in the homeostasis of T helper cell 1 (Th1), Th2 and regulatory T cells, initiated by changes or inactivation of innate immune cell.Manifestation of prenatal acclimatisation in the innate immune system with low inflammatory responses is the prime key leading to a tightly regulated postnatal adaptive immune responses. Understanding the mechanisms is crucial to develop strategies to prevent a further rise in diseases such as Type 1 Diabetes (T1D), Rheumatic arthritis and Systemic Lupus Erythematosus. To offer a significant insight and early guide intervention for many autoimmune disorders, therapeutic and manipulation of environmental triggers during clinical and pre-clinical stages is essential in identifying and attempting to remove them from the patient’s environment.Breast milk for instance, contains secretory immunoglobulin A antibodies which enhance the infant’s immune response and increases ?-cell proliferation protecting against the development of T1D.Setting down data about rate of occurrence and location allows us to comprehend certain environmental exposures and further moderation over time.