BACKGROUND: Children in low-income settings suffering from frequent diarrhoea episodes are also at a high risk of acute lower respiratory infections (ALRI). We explored whether this is due to common risk factors for both conditions or whether diarrhoea can increase the risk of ALRI directly. METHODS: We used a dynamic time-to-event analysis of data from two large child studies in low-income settings in Ghana and Brazil, with the cumulative diarrhoea prevalence over 2 weeks as the exposure and severe ALRI as outcome. The analysis was adjusted for baseline risk of ALRI and diarrhoea, seasonality and age. RESULTS: The child population from Ghana had a much higher risk of diarrhoea, malnutrition and death than the children in Brazil. In the data from Ghana, every additional day of diarrhoea within 2 weeks increased the risk of ALRI by a factor of 1.08 (95% CI 1.00-1.15). In addition, we found a roughly linear relationship between the number of diarrhoea days over the last 28 days and the risk of ALRI. In the Ghana data, 26% of ALRI episodes may be due to recent exposure to diarrhoea. The Brazilian data gave no evidence for an association between diarrhoea and ALRI. CONCLUSION: Diarrhoea may contribute substantially to the burden of ALRI in malnourished child populations.