Background: There is an international emphasis on providing timely and high quality data to monitor progress of countries toward Millennium Development Goals. Iran′s Multiple Indicator Demographic and Health Survey (IrMIDHS) aimed to provide valid information on population and health outcomes to monitor progress in achieving national priorities and health programs and to assist policy makers to design effective strategies for improving health outcomes and equity in access to care. Methods: A cross-sectional multi-stage stratified cluster-random survey is conducted through face-to-face household interviews. The sampling frame is developed using Iran′s 2006 population and housing census. Provincial samples ranging are from a minimum of 400 households per province to 6400 households in Tehran province. Cluster size is 10 households. The target sample includes 3096 clusters: 2187 clusters in urban and 909 clusters in rural areas. IrMIDHS instruments include three questionnaires: Household questionnaire, women aged 15-54 questionnaire, children under five questionnaire, supervision and quality assessment checklists and data collection sheets and standard weight and height measurement tools for under-five children. A cascading decentralized training method is used for training data collection and supervision teams. Quality assurance procedures are defined for the five steps of conducting the survey including: Sampling, training data collection and training teams, survey implementation, data entry and analysis. A multi-layer supervision and monitoring procedure is established. All the questionnaires are double entered. Conclusions: IrMIDHS will provide valuable data for policymakers in Iran. Designing and implementation of the study involve contributions from academics as well as program managers and policy makers. The collaborative nature of the study may facilitate better usage of its results.