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Background: Incidence of community acquired pneumonia is high globally. In Bangladesh, more male children than female children are brought to hospitals for pneumonia. We examined if there was disparities in the severity of illness and outcome by sex among children who were admitted with pneumonia to hospitals in Bangladesh. Methods: Hospitalized children, aged 2 to 59 months, meeting a case definition of pneumonia were recruited in seven hospitals following parental consent. At baseline, study doctors obtained socio-demographic characteristics and care seeking behaviors for pneumonia, and then clinical data were collected throughout the hospital stay. Multivariate analysis was performed to determine if the sex of the child had a relationship with either illness severity on admission or outcome in the hospital. Results: Between May 2004 and December 2008, 6,856 children, including 35% females, were recruited. A total of 1,371 (19.9%) children had non-severe pneumonia, 4,118 (60.0%) had severe pneumonia, and 1,367 (19.9%) had very severe pneumonia. A higher proportion of hospitalized females had very severe pneumonia as compared to males (21.5% versus 19.1%; P = 0.01), but there was no difference by sex in the proportion of children with severe or non-severe pneumonia. There was no difference by sex observed in the clinical management provided in the hospital, but a greater proportion of females (4.7%) as compared to males (3.6%) died in hospitals (P = 0.04). In multivariate analyses, female sex was associated with very severe pneumonia on admission (OR: 1.26, 95% CI: 1.09–1.47) and fatal outcome in the hospitals (OR: 1.31, 95% CI: 1.01–1.71). Death in female children admitted with very severe pneumonia was 4 times higher than that reported in males (OR: 4.37, 95% CI: 3.24–5.89). Conclusion: Our data demonstrates a sex-based disparity in the severity of pneumonia and deaths among children admitted to hospitals in Bangladesh, despite no existing disparity by sex in hospital treatment. These findings call for further investigations to explore the determinants of health seeking behavior by parents with children with pneumonia in a community that favors males to females, and to understand the role of differences by sex in childhood pneumonia outcomes in Bangladesh. [ABSTRACT FROM AUTHOR]