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Background: Endogenous endophthalmitis (EE) is a fulminant ocular disease. This study was conducted to explore frequent pathogens and significant prognostic factors associated with poor ocular outcomes. Materials and Methods: A retrospective analysis was performed in a tertiary hospital in Korea. Thirty-nine patients, treated between January 2000 and June 2017, were eligible for the analysis. Ocular outcomes were classified as follows: 1) no light perception (NLP), 2) light perception (LP), 3) hand motion (HM), 4) counting fingers (CF), and 5) 20/200 or better. Logistic regression and decision tree analyses were used to identify risk factors that were associated with poor outcomes. Results: Pathogens were identified in 23 (58.9%) samples from blood, liver aspirate, and/or vitreous humor. Klebsiella pneumoniae was the most frequent organism (12/39, 30.8%), followed by Candida species (3/39, 8.3%). The most common combined infection was liver abscess (16/39, 41.0%). Acute pyelonephritis occurred in 30.8% of cases (12/39). Final ocular outcomes were as follows: 35.9% (14/39) NLP, 15.4% (6/39) LP, 15.4% (6/39) HM, 7.7% (3/39) CF, and 25.6% (10/39) 20/200 or better. K. pneumoniae was a poor prognostic factor in univariate (odds ratio [OR], 13.3; 95% confidence interval [CI], 2.1-130.9) and multivariate (OR, 17.5; 95% CI, 2.1-398.8) regression analyses (NLP and LP vs. HM, CF, and 20/200 or better). Other factors did not reach statistical difference. Decision tree analysis identified K. pneumoniae as a node that divided ocular outcomes (P = 0.017). Conclusions: In conclusion, K. pneumoniae is the most frequent causative pathogen of EE. Considering the poor prognosis and rapid progression of K. pneumoniae EE, physicians should test for K. pneumoniae EE in patients who experience acute systemic infections with ocular signs and symptoms.