We diagnosed lower respiratory infection (LRI) due to Chlamydia trachomatis by retrospective serologic analysis in 10 of 47 (21%) study infants under 6 months of age hospitalized with bronchiolitis or pneumonia. These 47 infants represented all those on whom blood was available (76% of all 62 study infants under 6 months of age). Forty of these 47 infants had been followed from hospitalization for periods up to 5 years (mean, 26.3 months) for development of chronic illness. The patients with C. trachomatis LRI had significantly more reported chronic cough and abnormal lung function on follow-up than did those with LRI due to other agents or no agent found. C. trachomatis LRI patients also had more cough and wheeze than did a group of 71 age-matched normal infants. C. trachomatis LRI severe enough to require hospitalization may be associated with more chronic sequelae than is LRI due to other agents.