The objective of this study is to investigate the infection and distribution of Mycoplasma pneumoniae in autopsied pulmonary tissue of pediatric severe pneumonia. Mycoplasma pneumoniae nested polymerase chain reaction and immunohistochemistry were done on autopsy pulmonary tissue from 173 patients who died of severe pneumonia. Mycoplasma pneumoniae was identified in 135/173 (78.03%) and 114/173 (65.89%) samples of autopsied pulmonary tissue of lethal severe pneumonia via nested polymerase chain reaction and immunohistochemistry, respectively. The coincidence of both assays was 92.4%. Mycoplasma pneumoniae associated fatal pneumonia has showed an increasing trend from 1988 to 2005 in South China, and the fatality rate of Mycoplasma pneumoniae associated fatal pneumonia in infants, 1 to 12 months, has risen to 66.9% (97/145). Mycoplasma pneumoniae is a significant cause of severe pneumonia, it is a universal event in infants, and children have died of severe pneumonia in South China. Mycoplasma pneumoniae might be an important pathogen responsible for fatal pneumonia in Guangzhou area, South China.