Acute respiratory infections are the most important single cause of global burden of disease in young children globally and a major cause of child mortality. A recent review of studies reporting the incidence of acute lower respiratory infections (ALRI) in young children in the developing world was carried out by the WHO Child Health Epidemiology Reference Group in order to inform global burden of disease estimates. The review highlighted the low number of community-based longitudinal studies of ALRI incidence in young children which met minimum quality criteria. It underscored the need to give attention to issues of study design and the reporting of a basic minimum dataset which describes circumstances under which the studies were being conducted and the key design features of the study which may influence the ALRI estimate. This paper aims to provide methodological guidelines for the design, conduct, and reporting of epidemiological studies of ALRI in under-5s in developing countries. It discusses determinants of study quality related to both study design and statistical analysis and also issues requiring further research. It is hoped that these guidelines will stimulate further work in this field and encourage the publication of reports which contain sufficient data to permit a meaningful meta-analysis of the data, thus forming the basis of more reliable future estimates of global burden of ALRI.