•Defensins are peptides important in protecting the eye against endophthalmitis.•We demonstrate a genetic link between a genetic profile and endophthalmitis.•Focusing on culture positive cases is more successful at identifying links.•Genetic testing may help establish endophthalmitis risk in the future. Endophthalmitis is a sight threatening complication of intra-ocular procedures. It has been suggested that a predisposition to endophthalmitis is linked to a specific genotype in the human beta-defensin 1 (HBD-1) gene when previously analysed in a small UK cohort undergoing cataract surgery. We sought to test out this hypothesis in a larger international case: control study (centres in UK, Netherlands and Canada) following a variety of intraocular procedures. International case: control study 660 individuals undergoing an intraocular procedure were recruited (165 cases of endophthalmitis and 495 controls). DNA was extracted. Single nucleotide polymorphisms, SNPs, rs11362, rs1800972 and rs2702877 in the HBD-1 gene were analysed (both individual genotypes and haplotypes were obtained). No associations were found when individual SNPs were analysed across the combined international cohort. However, analysis of the Toronto sub-cohort, showed a statistically significant association between the endophthalmitis cohort and the rs1800972 C allele (OR: 3.18, CI: 1.32 - 7.68, p = 0.01) and rs2702877 G allele (OR: 3.06, CI: 1.35 - 6.95, p = 0.017). No haplotype association was identified with endophthalmitis compared to control in both institution sub-cohorts and combined cohort analysis. A strong trend associating the rs1800972, rs11362 GG mini-haplotype with culture positive endophthalmitis groups across all groups was noted, but this did not reach statistical significance. This is the first study to demonstrate a genetic link between a certain genetic profile (HBD-1 gene SNP variation) and endophthalmitis. Future pre-operative genetic testing could help identify patients at risk of endophthalmitis to guide invasive treatment options.