Narcolepsy is a chronic sleep disorder, likely with an autoimmune component. During 2009 and 2010, a link between A(H1N1)pdm09 Pandemrix vaccination and onset of narcolepsy was suggested in Scandinavia. In this study, we searched for autoantibodies related to narcolepsy using a neuroanatomical array: rat brain sections were processed for immunohistochemistry/double labeling using patient sera/cerebrospinal fluid as primary antibodies. Sera from 89 narcoleptic patients, 52 patients with other sleep-related disorders (OSRDs), and 137 healthy controls were examined. Three distinct patterns of immunoreactivity were of particular interest: pattern A, hypothalamic melanin-concentrating hormone and proopiomelanocortin but not hypocretin/orexin neurons; pattern B, GABAergic cortical interneurons; and pattern C, mainly globus pallidus neurons. Altogether, 24 of 89 (27%) narcoleptics exhibited pattern A or B or C. None of the patterns were exclusive for narcolepsy but were also detected in the OSRD group at significantly lower numbers. Also, some healthy controls exhibited these patterns. The antigen of pattern A autoantibodies was identified as the common C-terminal epitope of neuropeptide glutamic acidisoleucine/α-melanocyte-stimulating hormone (NEI/αMSH) peptides. Passive transfer experiments on rat showed significant effects of pattern A human IgGs on rapid eye movement and slow-wave sleep time parameters in the inactive phase and EEG θ-power in the active phase. We suggest that NEI/αMSH autoantibodies may interfere with the fine regulation of sleep, contributing to the complex pathogenesis of narcolepsy and OSRDs. Also, patterns B and C are potentially interesting, because recent data suggest a relevance of those brain regions/neuron populations in the regulation of sleep/arousal.arcolepsy is a chronic neurological disease characterized by irresistible daytime sleepiness (hypersomnia) and disturbed nocturnal sleep. Narcolepsy can be divided into two types: narcolepsy with cataplexy (NC) and narcolepsy without cataplexy. A typical feature of NC is sudden loss of muscle tone triggered by emotions (cataplexy). Other symptoms of narcolepsy are, for example, hypnagogic or hypnopompic hallucinations and sleep paralyses (1). The age of onset is usually around 12-16 y of age, but the disease is often diagnosed several years later (1). It affects ∼25-50 per 100,000 individuals, and the yearly incidence rate has been estimated to be around 1 per 100,000 person-y (2). Narcolepsy has a major negative impact on the quality of life, afflicting both physical and mental parameters (3). A major hallmark of narcolepsy (mostly NC) is the loss of hypocretin-1/ orexin-A (Hcrt/Orx), a neuropeptide hormone initially discovered independently by two groups (4, 5), by either a destruction of the orexinergic neurons or a selective down-regulation of Hcrt/Orx expression (6, 7). Consequently, a typical feature of NC is low levels (<110 pg/mL) of Hcrt/Orx peptide in the cerebrospinal fluid (CSF) (1).The causes of the loss of Hcrt/Orx and narcolep...