CHAIN is a multi-centre cohort study with a nested case control analysis of stored biological samples. Study sites are located in Africa and South Asia. Children will be recruited at admission to hospital, stratified by nutritional status. Exposures will be assessed at admission, during hospitalisation, at discharge, and at two time points after discharge. The main outcomes of interest are mortality, re-admission to hospital and failure of nutritional recovery up to 180 days after discharge. To determine community health norms, an additional sample of children living in the same communities will be enrolled and assessed at one time point only.