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Although Chlamydia trachomatis infection is common in pregnant women, such infections are rarely encountered in infants. To clarify the recognition of C. trachomatis infections in infants, we analyzed symptoms and signs of perinatally acquired chlamydial infection, together with its long-term prognosis in a large population-based patient series.A search through 2 national health registries covering 1996–2011, a cohort of 933,823 births, yielded 124 children with a microbiologically confirmed C. trachomatis infection. We then reviewed copies of the children’s medical records up to 16 years of age.One-third of the infants with chlamydial conjunctivitis (33/110) had spontaneous blood-stained discharge from the infected eye. The infants with C. trachomatis lower respiratory tract infection were mostly afebrile (30/32), and 15/32 of them had wheezing. Staccato cough was not recorded in any of the infants. The median diagnostic delay from the onset of the symptoms was 13 (range 4–374) days for conjunctivitis and 25 (range 10–149) days for lower respiratory tract infection. One neglected child developed bilateral corneal scars because of an untreated C. trachomatis infection.Blood-stained discharge was a typical finding in C. trachomatis conjunctivitis. The C. trachomatis–infected infants had severe and prolonged symptoms, but long-term consequences were rare. The diagnostic delay was long, especially among the infants with a C. trachomatis lower respiratory tract infection.