PURPOSE: Previous studies on fungal and bacterial keratitis were descriptive single case series analysis. We conducted a hospital-based retrospective study to evaluate fungal and bacterial keratitis using a case-control design to compare risk factors and clinical outcomes. METHODS: Twenty-nine cases of culture-positive fungal keratitis seen over a 5-year period were compared to 51 cases of culture-positive bacterial keratitis seen over a 21 months period. Using bacterial keratitis as the reference group, case-control odds ratios (OR) for predisposing factors and cohort relative risks (RR) for clinical outcomes associated with fungal keratitis were derived. Mantel-Haenszel adjustment procedures were used to examine the respective roles of confounding and intermediate variables. RESULTS: Compared to bacterial keratitis, fungal keratitis was significantly more likely to be associated with ocular trauma (OR = 2.69, 95% confidence interval [CI], 1.06-6.86) but significantly less likely to be associated with contact lens wear (OR = 0.16, 95% CI, 0.04-0.67) and preexisting ocular diseases (OR = 0.23, 95% CI, 0.07-0.72). Fungal keratitis was more likely to perforate than bacterial keratitis (RR = 5.28, 95% CI, 1.35-20.66) and to require penetrating keratoplasty (OR = 5.86, 95% CI, 2.06-16.69). CONCLUSIONS: Fungal keratitis appears more likely to result from ocular trauma, whereas bacterial keratitis is more likely to result from contact lens wear and pre-existing ocular diseases. Fungal keratitis is more likely than bacterial keratitis to result in perforation and require penetrating keratoplasty.