PURPOSE: To study the clinical and microbiological characteristics as well as the prognostic factors for post-filtering surgery endophthalmitis. METHODS: Twenty-three eyes were included in the study in four tertiary centres between 2004 and 2010. The clinical and microbiological data were collected prospectively (minimum follow-up, 6 months). Microbiological diagnosis was based on conventional cultures and panbacterial PCR (16SrDNA amplification and sequencing). RESULTS: The onset of endophthalmitis was early (<6 weeks) in 22 % of the cases and delayed in 78 %. Elevated intraocular pressure and hypopyon were more frequent in delayed than in early presentations (p = 0.04). By combining the results of culture and panbacterial PCR, a bacterial species could be identified in 73.9 % of the cases, including 56.5 % of commensal species of the digestive tract such as Moraxella spp., oropharyngeal streptococci and Enterococcus faecalis. Good final visual acuity (VA ≥ 20/40) was correlated with initial VA greater than light perception (p = 0.05). Poor final VA (≤20/400) was correlated with a higher virulence of the infecting bacterial species (p = 0.006), and was noted in all patients with early-onset endophthalmitis. CONCLUSION: Acute early- or delayed-onset post-filtering surgery endophthalmitis is frequently caused by bacteria of the digestive tract (e.g., Streptococcus and Enterococcus spp.). The combination of conventional cultures and panbacterial PCR allowed us to identify the causative microorganism in three-quarters of the cases, i.e., 21 % more cases than through culture alone. Despite adequate antibiotic and surgical treatment, the anatomical and visual prognosis remains poor.