Purpose: To identify the causative organisms and associated risk factors in cases of microbial keratitis (MK) presenting to Cairo University Hospitals.Setting: Tertiary care university centerMethods: A prospective study where corneal scrapings were obtained from 85 patients with MK over 9 months were subjected to direct smear examination using Gram and potassium hydroxide stains, and culture using blood, chocolate, MacConkey, and Sabouraud’s-dextrose agar. In culture-positive cases, antimicrobial sensitivity testing was performed.Results: From September 2020 to May 2021, 85 cases of MK were enrolled. Corneal scrapings were performed in 76 cases. A positive culture was obtained in 47 cases (61.8%). Among culture-positive cases, 36 cases (76.6%) were fungal, and 11 (23.4%) were bacterial. Among culture-negative cases (n=34), based on clinical appearance and response to antimicrobial therapy, 23 cases were considered fungal (67.6%), 6 bacterial (17.6%), and 5 due to acanthamoeba species (14.7%). Positive correlation was found between fungal etiology and previous herpetic keratitis (p=0.52), agricultural occupation (p=0.67), and ocular trauma of plant origin (p=0.11). A statistically significant correlation was found between presumed acanthamoebal etiology and contact lens wear (p<0.001).Conclusions: Positive culture was obtained in 61.8% of cases. Among these, 76.6% were fungal, and 23.4% were bacterial. In culture-negative cases, almost 70% were clinically presumed to be fungal, and the were considered either bacterial or acanthamoebal (approximately 15% each).