In 1911, Lindner and colleagues identified intracytoplasmic inclusions in infants with a nongonococcal form of ophthalmia neonatorum called inclusion conjunctivitis of the newborn (ICN). Mothers of affected infants were found to have inclusions in their cervical epithelial cells, fathers of such infants had inclusions in their urethral cells, and the epidemiology of sexually transmitted chlamydial infections was revealed. Fifty years later, chlamydial isolation procedures were developed, and studies again demonstrated Chlamydia trachomatis as an etiology of ICN and the female birth canal as the reservoir. In the late 1970s, a report by Beem and Saxon described respiratory tract colonization and a distinct pneumonia syndrome in infected infants. Genital chlamydial infection is recognized as the world's most common sexually transmitted disease, with estimates of greater than 4 million new infections occurring annually in the United States. Although most C. trachomatis infections in men and women are asymptomatic, infection can lead to severe reproductive complications in women. The high prevalence in women of child-bearing age results in exposure of an estimated 100,000 neonates in the United States annually. Many of these infants develop conjunctivitis, pneumonia, or both in the first few months of life. Clinical features, diagnosis, treatment, and approaches to prevention of conjunctivitis and pneumonia in the newborn and young infant are reviewed here. Appropriate testing for chlamydial infection in a pediatric victim of sexual assault and the implications of identifying C. trachomatis in suspected cases of childhood sexual abuse also are reviewed.