Purpose: To study the clinical and microbiological spectrum of endophthalmitis with emphasis on clinical features, visual outcomes and risks of surgical complications. Methods: A prospective observational study was conducted between 2012 and 2013 in a specific region in Denmark. Patients were clinically examined before, during and after surgical intervention for endophthalmitis. Results: Fifty eyes with endophthalmitis were included. Endophthalmitis after cataract surgery (post-cataract), anti-VEGF (vascular endothelial growth factor) intravitreal injections (post-injection) and cases of endogenous endophthalmitis were responsible for 40, 28 and 18% of all cases, respectively. There was no difference in the microbiological spectrum in post-cataract patients and post-injection patients, but patients with post-cataract endophthalmitis presented statistically significantly more frequently with hypopyon and fibrin in the anterior chamber. Between 20 and 25% of post-cataract and post-injection endophthalmitis patients developed a surgical complication after primary surgical intervention for endophthalmitis, and this was statistically significantly associated with a poor visual outcome. There was no statistically significant difference in the risk of surgical complications in phakic and pseudophakic eyes with post-injection endophthalmitis. Of the 8 patients with endogenous endophthalmitis, 67% developed a surgical complication, and these patients had a high mortality. The visual outcome in the most common types of endophthalmitis was good, with 60% of post-cataract patients achieving a visual outcome ≥0.5, and 64% of post-injection patients only had a mild vision loss (1-14 ETDRS letters) or even gained vision. Conclusions: The endophthalmitis cases had a broad clinical spectrum. Surprisingly, endogenous endophthalmitis accounted for almost one fifth of all cases. Patients with post-cataract endophthalmitis had a clinically different presentation than patients with post-injection endophthalmitis. In general, the bacteria were low-virulent and the visual outcomes good, but a substantial part of the patients developed a surgical complication which was associated with a poor visual outcome.