Neonatal conjunctivitis can be caused by a variety of pathogens, most commonly Chlamydia trachomatis, Neisseria gonorrhoeae, or other bacteria. Herpes simplex virus is a less common but potentially severe cause of viral conjunctivitis. Infants present with eyelid swelling, conjunctival injection, and discharge. The presentation of different pathogens overlaps significantly, and therefore a thoughtful diagnostic workup is imperative to guide appropriate therapy. Screening of pregnant women for sexually transmitted infections and prophylactic eye ointment for all newborns are critical aspects of preventative care.