Abstract: Objective To investigate the etiology of severe pneumonia in children in Chongqing. Methods The data of pathogen detection from 222 hospitalized children with sever pneumonia were retrospectively analyzed from January to December 2012. Results In 222 children, the deep airway specimens were cultured positive in 181 children (81.5%), 87 cases (48.1%) of bacterial infections, 22 cases (12.2%) of virus, 10 cases (5.5%) of fungi, 8 cases (4.4%) of mycoplasma pneumonia, one case (0.6%) of chlamydia trachomatis, and 53 cases (29.3%) of mixed infections. A total of 282 pathogen strains were identified in 181 positive children, 176 strains (62.4%) of bacteria including 140 strains of gram-negative bacteria and 36 strains of gram positive bacteria, with Klebsiella pneumoniae (43 strains) and Streptococcus pneumoniae (20 strains) being the most common, 70 strains (24.8%) of virus with respiratory syncytial virus (RAV, 43 strains) being the most common, 22 (7.8%) strains of fungi with Candida albicans being the most common, 13 (4.6%) strains of Mycoplasma pneumoniae, and one strain (0.4%)  of Chlamydia trachomatis. Bacteria strains were detected positive most often in autumn and winter, totally 40 cases (46.0%). Virus or mixed infections occurred mainly in winter and spring, 14 cases (63.6%) and 39 cases (73.6%) respectively. Virus infections were mainly in infants (one to 12 months old), while Mycoplasma pneumoniae infections were mainly in children aged 3-14 years. Among 181 children, 59 children received mechanical ventilation treatment, and 79 pathogen strains were detected. Different from children with non-mechanical ventilation, the gram positive bacteria were mainly Staphylococcus aureus and virus were mainly adenovirus in children with mechanical ventilation. Conclusions Severe pneumonias are mainly caused by bacterial infections in Chongqing and Klebsiella pneumoniae is the most common, followed by Streptococcus pneumoniae. Staphylococcus aureus and adenovirus infections should be considered in children with mechanical ventilation.