Objective:To analyze the risk factors of poor short-term outcome in patients with autoimmune encephalitis (AE).Methods:The data were collected retrospectively from patients hospitalized in the First Affiliated Hospital of Fujian Medical University from March 2016 to January 2021. According to the Modified Rankin Scale (mRS), eighty-one patients with AE were divided into the good prognosis group (mRS≤2, n=48) and the poor prognosis group (mRS>2, n=33). The clinical data, including the basic demographic data, main clinical manifestations, cranial MRI and electroencephalogram, as well as laboratory indicators from blood and cerebrospinal fluid (CSF), were compared between two groups, and the risk factors for poor outcome were analyzed by multivariate logistic regression. The receiver operating characteristic (ROC) curve was used to determine the cut-off value of these risk factors on predicting the poor short-term outcome for the AE patients. Results:The time of hospitalization was significantly longer in the poor prognosis group than in the good prognosis group ( P<0.05). Prevalence of severe disease course at admission, abnormal mental and behavior, δ wave and δ brush of abnormal EEG was significantly higher in the poor prognosis group than in the good prognosis group (all P<0.05). Serum leukocyte count, neutrophil count, lymphocyte count, mononuclear cell count, C-reactive protein, procalcitonin(PCT), alanine aminotransferase, aspartate transaminase, lactate dehydrogenase, creatine kinase, creatine kinase isoenzyme, apoA1/B, calcium, sodium, anion gap in serum, CSF oligoclonal bands, CSF-IgG index and antibody titer were significantly different between the two groups (all P<0.05). Severity of illness at admission ( OR=1.816, 95% CI 1.250-2.639, P=0.002), PCT ( OR=1.345, 95% CI 1.008-1.794, P=0.044), antibody titer in serum ( OR=1.422, 95% CI 1.071-1.888, P=0.015), CSF-IgG index ( OR=1.802, 95% CI 1.035-3.138, P=0.037) and anionic gap ( OR=1.640, 95% CI 1.191-2.259, P=0.002) were the independent risk factors for the poor short-term prognosis of patients with AE. The AUC value of combing the above 5 indexes to predict the poor short-term prognosis in patients with AE was 0.920 (95% CI 0.834-0.971), with 83.87% sensitivity and 88.37% specificity. Conclusion:Severity of illness at admission, PCT, antibody titer in serum, CSF-IgG index and anionic gap are the independent risk factors of poor short-term prognosis in patients with AE and the combination of these 5 indexes can sufficiently predict the poor short-term prognosis in patients with AE.