The International Study of Asthma and Allergies in Childhood (ISAAC) programme commenced in 1991 to study the aetiology of asthma, allergic rhinoconjunctivitis and atopic eczema in children in different populations using standardised methodology and facilitating international collaboration. ISAAC Phase One (1992-1996) found marked differences in the prevalence of symptoms of asthma and allergic disease throughout the world which have not been explained by the current understanding of these diseases. ISAAC Phase Two (1998-2004) uses intensive investigations to further examine the potential role of risk and protective factors that may contribute to the international difference observed in Phase One. Phase Three (2000-2003) essentially represents a repeat of Phase One, in which more detailed standardised data are obtained to enable the time trends of symptom prevalence to be determined as well as the development of a more comprehensive 'world map'. The ISAAC Phase Three rationale and methods are described in this paper. With over 280 centres in 106 countries, we anticipate that ISAAC Phase Three will comprehensively determine the prevalence of symptoms of asthma and allergic disease worldwide, explore recent time trends in the prevalence of these symptoms and cast new light on the aetiology of asthma and allergic disease.