Special studies and isolated initiatives over the past several decades in low-, middle- and high-income countries have consistently shown inequalities in health among socioeconomic groups and by gender, race or ethnicity, geographical area and other measures associated with social advantage. Significant health inequalities linked to social (dis)advantage rather than to inherent biological differences are generally considered unfair or inequitable. Such health inequities are the main object of health development efforts, including global targets such as the Millennium Development Goals, which require monitoring to evaluate progress. However, most national health information systems (HIS) lack key information needed to assess and address health inequities, namely, reliable, longitudinal and representative data linking measures of health with measures of social status or advantage at the individual or small-area level. Without empirical documentation and monitoring of such inequities, as well as country-level capacity to use this information for effective planning and monitoring of progress in response to interventions, movement towards equity is unlikely to occur. This paper reviews core information requirements and potential databases and proposes short-term and longer term strategies for strengthening the capabilities of HIS for the analysis of health equity and discusses HIS-related entry points for supporting a culture of equity-oriented decision-making and policy development.