Autoimmune diseases (AIDs) result in high levels of various autoantibodies in the serum as well as systemic inflammation and targeted organ damage. The incidence of AID has increased over recent decades. Glycosylation is a significant part of the post-translational modification of proteins and has been recognised as an important part of immune regulation in humans. Aberrant glycosylation manifests as pro- or anti-inflammatory effects. Numerous studies have confirmed that aberrant glycosylation plays a crucial role in the AID process. The development of emerging technologies such as the lectin microarray has facilitated research on the structure and function of glycans and glycosylation. Newly developed devices allow for high-throughput, high-speed, and highly specific research on aberrant glycosylation. Here, we review the role of glycosylation in the regulation of effector function in the context of autoimmunity and aberrant glycosylation in AIDs. This paper also discusses emerging technologies and clinical applications of glycosylation.