BACKGROUND: The reduction of health inequalities is a long-standing public health priority. Accurate and timely measurement of the magnitude of health inequalities over time is complex, often relying on data available from a decennial census to conduct detailed analyses of social and geographical inequalities. While inequalities in mortality rates and life expectancy are well-established, the scale of inequality in health expectancies has been reported to be even greater. This study examines changes in inequality in disability-free life expectancy (DFLE) over time between Lower Super Output Areas (LSOAs) in England, grouped into quintiles of an area-based measure of relative deprivation. METHODS: Life expectancy (LE) and DFLE for males and females at birth and at age 65 were estimated using a combination of survey, mortality and population data; survey data provided an estimate of the prevalence of limiting long-standing illness or disability (LLSI) used in the DFLE metric. An estimate of the inequality in DFLE between area-based quintiles of relative deprivation (using the Index of Multiple Deprivation 2007) in the periods 2001-04 and 2005-08 enabled the measurement of change in equality over time between advantaged and disadvantaged areas. RESULTS: The prevalence of LLSI among males and females rose incrementally with increasing levels of deprivation in both periods. Males and females in the most deprived areas were more than 1.5 times more likely to report LLSI compared to those in the least deprived areas. There were also large inequalities in LE and DFLE in a similar pattern to LLSI. The extent of inequality in DFLE between the most and least deprived quintiles was approximately twice that of LE. Although LE and DFLE generally increased over time, this improvement varied across quintiles, causing the gap between the most and least deprived quintiles to increase. In comparison with more advantaged areas, people experiencing the greatest deprivation spent the greatest proportion of their lives with a limiting illness or disability, and this proportion increased over time. CONCLUSIONS: Males and females at birth and at age 65 in the less deprived areas could expect longer, healthier lives than their counterparts in more deprived areas in both 2001-04 and 2005-08. This analysis suggests that the inequality in DFLE between deprived and affluent area clusters has increased during the first decade of the 21st century.