Background We describe 12 cases of chlamydial ophthalmia neonatorum and the current scientific evidence on its prevention and treatment. The data presented were obtained from the “Maduo” study, a prospective observational study of the relationship between curable sexually transmitted infections and adverse neonatal outcomes at four antenatal clinics in Gaborone, Botswana. Methods Infants of mothers with perinatal chlamydia infection were evaluated for chlamydial ophthalmia neonatorum based on clinical presentation of conjunctivitis or positive test via GeneXpert CT/NG assay. Data on 29 infants born to mothers with postnatal C. trachomatis infection were analysed. Results 12 infants were diagnosed with chlamydial ophthalmia neonatorum. Eight of those cases were confirmed with the GeneXpert CT/NG assay while four were identified as probable cases based on clinical history and presentation. Overall, nine infants presented with signs of conjunctivitis, while three who had a positive diagnostic test result had asymptomatic infection. All but one infant had received ocular 1% tetracycline prophylaxis at birth, and four infants had signs suggestive of chlamydial pneumonia at presentation. Two out of five symptomatic cases whose mothers reported completion of their treatment course with erythromycin had lingering symptoms. Conclusions Our findings affirm that the current prophylaxis and treatment modalities for chlamydial ophthalmia neonatorum are inadequate. To the extent feasible in low- and middle-income countries, we recommend implementation of routine C. trachomatis screening and treatment in pregnant women.