We present a comparison between serology and genetic detection of three bacterial pathogens causing lower respiratory tract infection (LRI). We evaluated serology and PCR for the detection of Mycoplasma pneumoniae, Bordetella pertussis and Chlamydia pneumoniae from 1712 nasopharyngeal and serum samples. For 856 nasopharyngeal samples, average PCR time was 7.2 days, the parallel serum samples was 13 days. Automated extraction of nucleic acids reduces average PCR time to 6.7 days.