An incorrect or late diagnosis can lead to an increase in the morbidity and mortality caused by pneumonia, and the availability of a rapid and accurate microbiological test to verify the aetiology is imperative. This study evaluated a molecular test for the identification of the bacterial cause of atypical community-acquired pneumonia (ACAP). Fifty-four children with pneumonia were studied using bacteriological cultures, Mycoplasma pneumoniae, Coxiella burnetii, Chlamydophila pneumoniae and Legionella spp. serology, and Streptococcus pneumoniae and Legionella antigens. Simultaneously, the presence of bacterial and fungal DNA was tested for in respiratory secretion samples using the Vircell SL kit, including multiplex PCR and amplicon detection by means of line blots. There were 14 cases of ACAP caused by M. pneumoniae, with positive kit results for 13 of them, and two cases of Q-fever, with negative kit results for Coxiella burnetii. The test was negative in the remaining 38 cases (one staphylococcal pneumonia, 20 Streptococcus pneumoniae pneumonias, and 17 probable viral pneumonias). The sensitivity of the test for the detection of M. pneumoniae was 92.8% and the specificity was 100%. The Vircell SL kit allows detection of M. pneumoniae DNA in respiratory secretion samples from children with ACAP.