Gangliosides are structurally and functionally polymorphic sialic acid containing glycosphingolipids that are widely distributed in the human body. They play important roles in protecting us against immune attacks, yet they can become targets for autoimmunity and act as receptors for microbes, like the influenza viruses, and toxins, such as the cholera toxin. The expression patterns of gangliosides vary in different tissues, during different life periods, as well as in different animals. Antibodies against gangliosides (AGA) can target immune attack e.g., against neuronal cells and neutralize their complement inhibitory activity. AGAs are important especially in acquired demyelinating immune-mediated neuropathies, like Guillain-Barré syndrome (GBS) and its variant, the Miller-Fisher syndrome (MFS). They can emerge in response to different microbial agents and immunological insults. Thereby, they can be involved in a variety of diseases. In addition, antibodies against GM3 were found in the sera of patients vaccinated with Pandemrix®, who developed secondary narcolepsy, strongly supporting the autoimmune etiology of the disease.