Multiple sclerosis (MS) is a complex autoimmune disorder that affects the central nervous system. Although the pathological mechanisms of MS have been extensively studied, its association with other autoimmune diseases, known as comorbidities, remains unclear. In this comprehensive review article, we aim to clarify the cellular and molecular relationship between MS and the incidence of organ-specific autoimmune comorbidities by summarizing former studies. We will explore the commonalities and possible differences between the immune response mechanisms in MS and other autoimmune diseases and provide an overview of the current understanding of the pathophysiological processes involved in the co-occurrence of MS and other organ-specific autoimmune comorbidities. Through this review, we aim to contribute to the development of effective therapeutic strategies that can improve the quality of life of MS patients with comorbidities.