Background Many cities in developing countries experience an unplanned and rapid growth. Several studies have shown that the irregular urbanization and equipment of cities produce different health risks and uneven exposure to specific diseases. Consequently, health surveys within cities should be carried out at the micro-local scale and sampling methods should try to capture this urban diversity. Methods This article describes the methodology used to develop a multi-stage sampling protocol to select a population for a demographic survey that investigates health disparities in the medium-sized city of Bobo-Dioulasso, Burkina Faso. It is based on the characterization of Bobo-Dioulasso city typology by taking into account the city heterogeneity, as determined by analysis of the built environment and of the distribution of urban infrastructures, such as healthcare structures or even water fountains, by photo-interpretation of aerial photographs and satellite images. Principal component analysis and hierarchical ascendant classification were then used to generate the city typology. Results Five groups of spaces with specific profiles were identified according to a set of variables which could be considered as proxy indicators of health status. Within these five groups, four sub-spaces were randomly selected for the study. We were then able to survey 1045 households in all the selected sub-spaces. The pertinence of this approach is discussed regarding to classical sampling as random walk method for example. Conclusion This urban space typology allowed to select a population living in areas representative of the uneven urbanization process, and to characterize its health status in regards to several indicators (nutritional status, communicable and non-communicable diseases, and anaemia). Although this method should be validated and compared with more established methods, it appears as an alternative in developing countries where geographic and population data are scarce.