Background This study highlights changing disagreement between census and death record information in the reporting of the education of the deceased and shows how these reporting differences influence a range of mortality inequality estimates.

Methods This study uses a census-linked mortality data set for Estonia for the periods 2000–2003 and 2012–2015. The information on the education of the deceased was drawn from both the censuses and death records. Range-type, Gini-type and regression-based measures were applied to measure absolute and relative mortality inequality according to the two types of data on the education of the deceased.

Results The study found a small effect of the numerator–denominator bias on unlinked mortality estimates for the period 2000–2003. The effect of this bias became sizeable in the period 2012–2015: in high education group, mortality was overestimated by 23–28%, whereas the middle education group showed notable underestimation of mortality. The same effect was small for the lowest education group. These biases led to substantial distortions in range-type inequality measures, whereas unlinked and linked Gini-type measures showed somewhat closer agreement.

Conclusions The changing distortions in the unlinked estimates reported in this study warn that this type of evidence cannot be readily used for monitoring changes in mortality inequalities.