Alternative splicing plays an important role in the pathogenesis, diagnosis, treatment and prognosis of autoimmune diseases. Alternative splicing is universal and non-preferred in autoimmune diseases, and exon skipping is the most common type in alternative splicing types. The occurrence and development of autoimmune diseases can be influenced by the 5′ splicing, 3′ splicing, number change of exons, splicing affected by the single nucleotide polymorphism and the variance of gene expression levels. Moreover, different single nucleotide polymorphisms of the same gene can affect the development of various autoimmune diseases. This review summarizes the role of different forms of alternative splicing in various autoimmune diseases, and aims to provide a basis for further study of the conditions in different development stages of autoimmune diseases and the regulatory mechanism of different levels of splicing isoforms.