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Background  Atypical pathogens such as  Mycoplasma pneumoniae ,  Chlamydophila pneumoniae , and  Legionella pneumophila  are increasingly recognized as important causes of community acquired pneumonia (CAP) worldwide. Such etiological data for Vietnam is scarce and clinical doctors lack accurate information on which to base their diagnosis and treatment of pneumonia. This study identifies the prevalence and risk factors of severe community acquired pneumonia due to these atypical pathogens (severe- Ap CAP) in children aged 1–15 years with CAP in a pediatric hospital in Hanoi, Vietnam.    Methods  722 hospitalized children with CAP were recruited for detecting those atypical pathogens, using multiplex PCR and ELISA. Clinical and epidemiological data were collected. Multivariate logistic-regression analyses were performed to evaluate the associations of potential risk factors with severe- Ap CAP.    Results  Among 215 atypical pathogen-positive CAP cases, 45.12% (97/215) were severe- Ap CAP. Among the severe- Ap CAP group, 55.67% (54/97) cases were caused by pure atypical pathogens and 44.33% (43/97) resulted from a co-infection with typical respiratory pathogens.  M. pneumoniae  was the most common, with 86.6% cases (84/97) in the severe- Ap CAP group, whereas  C. pneumoniae  and  L. pneumophila  were less frequent (6.19% and 7.22%, respectively). The highest rate of severe- Ap CAP was in children younger than two years (65.98%). The differences related to age are statistically significant ( P  = 0.008).  The factors significantly associated with severe- Ap CAP were age (OR = 0.84, 95% CI = 0.75-0.93,  P  = 0.001), co-infection with typical bacteria (OR = 4.86, 95% CI = 2.17-10.9,  P  < 0.0001), co-infection with respiratory viruses (OR = 4.36, 95% CI = 1.46-13.0,  P  = 0.008), respiratory/cardiac system malformation (OR = 14.8, 95% CI = 1.12 -196,  P  = 0.041) and neonatal pneumonia (OR = 11.1, 95% CI = 1.06 -116,  P  = 0.044).    Conclusions  Severe- Ap CAP presented at a significant rate in Vietnamese children. More than 50% of severe- Ap CAP cases were associated with pure atypical pathogen infection.  M. pneumoniae  appeared most frequently. The highest rate of severe- Ap CAP was in children younger than two years. Younger age and co-infection with typical bacteria or viruses were the most significant risk factors, while respiratory/cardiac system malformation and neonatal pneumonia were additional potential risk factors, associated with severe- Ap CAP in Vietnamese children.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2458-14-1304) contains supplementary material, which is available to authorized users.

First report on prevalence and risk factors of severe atypical pneumonia in Vietnamese children aged 1–15 years