Changes in health socio-economic inequalities are currently measured by comparing the mortality gradient across aggregates of small administrative areas at two points in time. However, this methodology may be flawed as it ignores population movement, which previous research has shown to be selective, with a net loss of the more affluent (and possibly healthier) residents from deprived to more affluent areas. This paper investigates whether selective migration contributed sufficiently to the observed socio-economic gradients in mortality in England and Wales throughout the 1990s so as to invalidate the current method of monitoring health inequalities. The ONS Longitudinal Study for England and Wales was used to calculate directly standardised mortality rates (DSR) by decile of deprivation in 1991 and 2001. The DSRs for 2001 were calculated twice, once according to decile of residence in 2001, and also according to the original decile in 1991. Selective migration was found to make an important contribution in explaining increases in inequalities between areas, accounting for about 50% of the increase for those aged less than 75. At the older age groups, however, selective migration was responsible for a narrowing of mortality differentials over time. These results indicate that caution should be exercised when using repeated ecological studies in assessing the extent of changes in inequalities over time.