A number of recent studies have highlighted the potential contribution of migration to increasing inequalities in health between areas with different levels of deprivation. Some of these studies have reported that increasing inequalities between areas can, at least partly, be explained by selective migration. Both mortality and morbidity have been used as indicators of health status, but many of the studies focusing on morbidity have suffered from specific methodological problems, including the use of self-reported health measured after migration had occurred, thereby ignoring the possible effect that migration itself may have on health and the reporting of health. This study used general practice records assessed prior to movement, an arguably more objective measure of health status, from 40 general practices, to determine whether selective migration influenced the distribution of health in Northern Ireland between the years 2000 and 2005. Evidence of selective migration was found in the study, with migrants often having significantly different levels of health to non-migrants. However, overall migration within this cohort did not substantially alter the distribution of health through time, partly because the migrants out of the deprived and affluent areas were replaced by in-migrants with similar levels of health. The absence of an effect of migration in this instance should not be used, however, to conclude that migration effects are unimportant in assessing changes in inequalities through time. Rather, migration should be viewed in the context of the underlying population dynamics, which at the time of this study were characterised by a process of urban regeneration. Varying population movements, operating at different times and locations, require that the effects of migration be considered in all studies which examine changes in the spatial distribution of health.