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To compare infectious organisms and visual outcomes of endophthalmitis after intravitreal injection (IVI) with endophthalmitis after pars plana vitrectomy (PPV).Retrospective, comparative, consecutive case series of patients diagnosed with presumed infectious endophthalmitis after IVI of an anti-vascular endothelial growth factor medication or PPV between January 1, 2009, and October 1, 2012, from one center. Main outcome measures were infectious organism and final visual acuity.Forty-four cases of presumed infectious endophthalmitis (17 culture positive) occurred after IVI and 19 cases (9 culture positive) occurred after PPV. Of note, 56.3% of culture-positive IVI cases were due to bacteria associated with oral flora, primarily Streptococcus species, compared with none in the PPV group (P = 0.01). There was a trend approaching significance for IVI patients to have lost ≥3 lines of visual acuity compared with PPV patients at final follow-up (P = 0.07). Within the IVI group, patients were more likely to have lost ≥6 lines of visual acuity at final follow-up when endophthalmitis was due to an organism associated with oral flora (P = 0.007).Endophthalmitis after IVI has a higher likelihood of being due to oral flora compared with endophthalmitis after PPV. Among IVI patients, worse visual outcomes occurred when endophthalmitis was due to oral flora.