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Background Brain magnetic resonance imaging (MRI) abnormalities are an important finding in the evaluation of patients with suspected autoimmune encephalitis (AE). There have been few studies evaluating the frequency and prognostic significance of MRI abnormalities, especially hippocampal swelling, in anti- N-methyl-D-aspartate receptor (NMDAR) and anti-leucine-rich glioma-inactivated 1 (LGI1) Ab-mediated encephalitides.Methods Adult patients with confirmed antibody-mediated encephalitis and at least one MRI scan were prospectively and retrospectively recruited from ten Australian hospitals (n=139). MRI scans were evaluated by a neuroradiologist blinded to the specific AE diagnosis. We evaluated associations between acute MRI abnormalities (e.g., hippocampal swelling) with 12-month function (modified Rankin scale, mRS >2 = worse outcome) and radiological findings.Results In patients with anti-LGI1 Ab-mediated encephalitis, hippocampal swelling on initial MRI was associated with worse function at 12 months (OR 0.03; 95% CI 0.003, 0.34; p = 0.005). Initial AE-associated T2/fluid attenuated inversion recovery (FLAIR) hyperintensities were not associated with 12-month mRS in either the anti-NMDAR (OR 0.39; 95% CI 0.04, 3.97; p = 0.42) or anti-LGI1 Ab-mediated encephalitis groups (OR 0.34; 95% CI 0.07, 1.57; p = 0.17). In anti-LGI1 Ab-mediated encephalitis, both hippocampal swelling (OR 5.76; 95% CI 1.14, 29.01; p = 0.03) and T2/FLAIR hyperintensity (OR 8.97; 95% CI 1.65, 49.01; p = 0.01) were related to the development of mesial temporal atrophy.Conclusion Acute hippocampal swelling is associated with worse outcomes in anti-LGI1 Ab-mediated encephalitis and, alongside initial T2/FLAIR hyperintensity, is associated with the development of mesial temporal atrophy.