OBJECTIVE: Initiatives to monitor progress in health interventions like sanitation are increasingly focused on disparities in access. We explored three methodological challenges to monitoring changes in sanitation coverage across socio-economic and demographic determinants: (i) confounding by wealth indices including water and sanitation assets, (ii) use of individual urban and rural settings versus national wealth indices and (iii) child-level versus household-level analyses. METHODS: Sanitation coverage by wealth for children and households across settings was estimated from recent Demographic and Health Surveys in six low-income countries. Household assignment to wealth quintiles was based on principal components analyses of assets. Concordance in household quintile assignment and estimated distribution of improved sanitation was assessed using two wealth indices differing by inclusion or exclusion of water and sanitation assets and independently derived for each setting. Improved sanitation was estimated using under five children and households. RESULTS: Wealth indices estimated with water, and sanitation assets are highly correlated with indices excluding them but can overstate disparities in sanitation access. Independently, derived setting wealth indices highly correlate with setting estimates of coverage using a single national index. Sanitation coverage and quintile disparities were consistently lower in household-level estimates. CONCLUSIONS: Standard asset indices provide a reasonably robust measure of disparities in improved sanitation, although overestimation is possible. Separate setting wealth quintiles reveal important disparities in urban areas, but analysis of setting quintiles using a national index is sufficient. Estimates and disparities in household-level coverage of improved sanitation can underestimate coverage for children under five.