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In many studies, health expectancies (HE) by relative socio-economic status have been calculated but the estimation of confidence intervals and the performance of tests of significance for differences in HE between sub-populations have been impeded by lack of variance estimation methods. Also in most scenarios, the sampling designs of the surveys from which prevalence of ill-health conditions are obtained have been ignored. This paper aims at presenting variance estimation techniques such as the bootstrap and the delta method taking account of the survey design. The study suggests that using the raw survey data and the Delta method while accounting for the survey design, gives better estimates for the variance compared to the bootstrap method and therefore is a highly recommended method for variance estimation of HE by relative socio-economic status.