AIM: To evaluate the conjunctival bacterial flora and their antibiotic resistance profile in diabetic patients attending Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife so as to determine the most appropriate antibiotic prophylaxis. MATERIALS AND METHODS: This was a descriptive, cross-sectional study. Simple random sampling technique was used to recruit 88 diabetic patients coming for follow up at the Endocrinology clinic of the Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife over a period of four (4) months. Information on their sociodemographic data and diabetic history was obtained and recorded in the proforma. Their latest Fasting blood sugar and Hemoglobin A1c levels were determined. Conjunctival swabs were taken from the eye of each diabetic patient, for microscopy, culture and sensitivity testing in the microbiology laboratory. Similarly, conjunctival swabs were taken from 88 age-matched non-diabetic subjects for comparison. Results obtained were recorded in the proforma and subsequently input in the computer for data analysis. Data was analyzed with the Statistical Package for Social Sciences (SPSS) version 16 and presented as charts and tables.