Objective: To measure the frequency of ophthalmia neonatorum among all babies born in MCH Center, PIMS (Pakistan Institute of Medical Sciences), Islamabad, in one month's time and to determine their causative organisms. Study Design: An observational study. Place and Duration of Study: The MCH Center, PIMS, during the month of November 2008. Methodology: All babies born from 1st to 30th November, 2008 in the MCH Center, PIMS, Islamabad, Pakistan were included in the study. All babies were examined for signs of conjunctivitis on days 1, 3, 7, 14, 21 and 28 of life. Conjunctival swabs were taken for gram staining and culture from those with clinical diagnosis of conjunctivitis. Frequency of known maternal and neonatal risk factors for the disease were assessed. Proportions were compared using chi-square test with significance at p < 0.05. Results: Seventeen percent of the 1010 babies developed conjunctivitis. Staphylococcus aureus (65% of all positive cultures) was the most common causative organism. No case of gonococcus was isolated. Meconium stain liquor (p=0.004) and caesarain section (p < 0.001) were found to be the most frequent associated conditions in conjunctivitis. Conclusion: There was a high frequency of neonatal conjunctivitis, with Staphylococcus aureus as the most common causative agent. Poor hygienic conditions and practices could be an important risk factor in Pakistan.