Aim and objectives: To determine the normal conjunctival bacterial flora and the effect of 5% povidone-iodine on the flora among patients attending the out patient clinics of the Guinness Eye Centre; Onitsha, Nigeria. Materials and methods: New adult patients attending the Guinness Eye Centre, Onitsha were recruited using simple random sampling technique. Microscopy, culture and sensitivity of conjunctiva and lid margin swabs were performed to identify the bacterial organisms and determine their antibiotic susceptibility. The specimens were cultured in chocolate, nutrient and MacConkey agar. The bacterial colonies were counted. After the collection of the lid and conjunctival swabs, 5% povidone-iodine was instilled into the lower conjunctival fornix and swabs collected from it at one minute, five minutes and ten minutes interval. The specimens collected post povidone-iodine instillation were also cultured and bacterial colonies also counted.