Chlamydophila pneumoniae was frequently found in bronchial secretions of children with therapy-refractory bronchitis or pneumonia. It was studied, how the agent modifies the course of disease and what findings are associated with the infection. Bronchial secretions obtained at bronchoscopy of 428 children were studied for C. pneumoniae infection using polymerase chain reaction with enzyme immunoassay detection. Children tested negative and positive were compared for their clinical findings. C. pneumoniae was found in 143 children (33 %). A C. pneumoniae infection has been found to be associated with a purulent bronchial inflammation (90/143 vs. 144/285, p = 0.02), a Streptococcus pneumoniae co-infection (13/143 vs. 6/285, p = 0.002) and a restrictive disturbance (11/51 vs. 8/93, p = 0.04). Purulent inflammation (Odds ratio 7.9; 95 % confidence interval [CI] 1.6-39.3), 2 co-infections (Odds ratio 14.3; 95 % CI 1.4-144.4) and co-infection with M. pneumoniae (4/4 versus 9/26, p = 0.03; Mantel Haentzel 3.0; 95 % CI 1.1-8.0) were identified as factors more often associated with a restrictive disturbance in children with bronchial C. pneumoniae infection. An adequate antibiotic therapy improved pulmonary function. No association was found for wheezing, eosinophil inflammation of the nasal mucosa, alpha-1 antitrypsin or immunoglobulin deficiency in serum, level of secretory IgA in bronchial mucus, pathological lung scintigram, gastro-esophageal reflux disease, sweat test and other co-infections. In children with therapy-refractory bronchitis or pneumonia bronchial C. pneumoniae infection was associated with a more severe disease in case of several, mostly bacterial co-infections. Adequate antibiotic therapy for C. pneumoniae infection has been demonstrated to improve pulmonary function.