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Notes: To evaluate the role of Chlamydia pneumoniae respiratory tract infection on pediatric asthma, allergic rhinitis or atopic eczema initiation, children of three age groups (n = 1211) were prospectively studied for a C. pneumoniae infection using throat swabs and polymerase chain reaction (PCR) with enzyme immunoassay (EIA) detection. Infected children (study group, SG) were examined monthly until the agent could not be detected, quantifying persistent infection. They were compared with randomly selected, non-infected children without asthma matched for age, gender and origin (control group, CG) regarding lung function and inflammatory parameters as well as initiation of allergic diseases judged by family doctor diagnosis after, in median, 22 months. At the first follow-up examination, SG children revealed a higher leukotriene B4 (median 36 pg/ml vs. 19, p = 0.04) and 8-isoprostane (median 15 pg/ml vs. 12, p = 0.04) in breath condensate characterizing neutrophil, agent-related inflammation and oxidative stress in the lower airways. Cysteinyl leukotrienes, important in acute allergic inflammation, were without difference. Local, anti C. pneumoniae secretory immunoglobulin A antibodies were higher in children after C. pneumoniae infection (optical density median 0.7 vs. 0.4, p = 0.001) confirming PCR–EIA results. At the final examination, there was no difference in pathological lung function tests, parameters of exhaled breath condensate or eosinophilia of the nasal mucosa. Incidence of asthma (0/55 vs. 5/54, p = 0.03) and allergic rhinitis [3/53 vs. 10/52, p = 0.04, odds ratio and 95% confidence interval-OR 0.25 (0.06;0.98)] as well as prevalence of asthma [1/56 vs. 9/58, p = 0.02, OR 0.1 (0.01;0.81)] and allergic rhinitis [6/56 vs. 16/58, p = 0.03, OR 0.32 (0.11;0.88)] were lower in the SG children. There was no association in atopic eczema. Three children with persistent infection revealed a slightly higher incidence in allergic rhinitis without significance than those with single C. pneumoniae detection (1/3 vs. 2/50), however, not to the CG. In conclusion a C. pneumoniae upper respiratory tract infection may be regarded as a protective factor for childhood asthma or allergic rhinitis in a population of kindergarten and school-age children.