ObjectiveTo determine the aetiology of community acquired pneumonia in children presenting to primary care in Northern Malawi, and to ascertain predictors for identification of children requiring hospitalisation.DesignThe BIOmarkers TO diagnose PnEumonia study was a prospective cohort study conducted from March to June 2016.SettingPrimary care in Northern Malawi.Patients494 children aged 2 –59 months with WHO defined pneumonia.Main outcome(s) and measure(s)Number of children with bacterial infection identified and the sensitivity/specificity of WHO markers of severity for need for hospitalisation.Results13 (2.6%) children had a bacterium consistent with pneumonia identified. A virus consistent with pneumonia was identified in in 448 (90.7%) of children. 56 children were admitted to hospital and two children died within 30 days. 442 (89.5%) received antibiotic therapy. Eleven children (2.6%) had HIV. WHO severity markers at baseline demonstrated poor sensitivity for the need for hospitalisation with a sensitivity of 0.303 (95% CI 0.188 to 0.441) and a specificity 0.9 (95% CI 0.868 to 0.926). A prediction rule to indicate the need for hospitalisation was developed.Conclusions and relevanceThe low rate of bacterial infection and high use of antibiotics in the setting of high immunisation rates highlights the changing profile of childhood pneumonia. Similarly, the markers of need for hospitalisation may have changed in the setting of extended immunisation. Further studies are required to examine this.