BACKGROUND:Autoimmune encephalitis is characterized by neuropsychiatric symptoms associated with brain inflammation. The differential is usually broad and Psychiatry often collaborates with Neurology in diagnostic clarification and symptom management. At least 40% of neuroencephalitis cases are of unknown etiology which adds to difficulties in making the right diagnosis and deciding on the appropriate treatment (Granerod et al., Lancet Infect Dis 10:835-44, 2010). The aim of this case series was to present four cases with complicated psychiatric symptomatology and isolated neurologic signs and symptoms, evaluated at a large tertiary medical center and treated for suspected autoimmune encephalitis, demonstrating the complexity of diagnosis and treatment. CASE PRESENTATION:Four diagnostically challenging and heterogeneous cases displayed clinical symptomatology suggestive of autoimmune encephalitis. All cases presented with neurologic and psychiatric symptoms, but had negative autoantibody panels, normal or inconclusive magnetic resonance imaging results and non-specific cerebrospinal fluid changes. All were challenged with immunosuppressive/immunomodulatory treatments with overall poor response rates. CONCLUSIONS:There is a heterogeneous presentation of autoimmune encephalitis in pediatric populations. In the absence of positive findings on testing, individuals who do not meet proposed criteria for seronegative encephalitis may be misdiagnosed, and/or may not respond adequately to treatment. In those cases, comprehensive evaluation and stringent application of consensus guidelines is necessary.