The Healthy Life Years (HLY) indicator is the official European Union indicator and a cornerstone of many health policies used in over 15 countries in the EU region to set national health plans and monitor targets. It is also used to investigate trends over time in the proportion of total life years spent in good or poor health, socioeconomic inequalities in health and mortality and the male-female health survival paradox. Based on the Global Activity Limitation Indicator (GALI) included in the European Union Statistics on Income and Living Conditions (EU- SILC), a great amount of effort has been directed at harmonising and making HLY comparable across countries. Nonetheless, the characteristics of the age-specific prevalence distribution are still rarely accounted for, regardless of the fact that patterns of prevalence often fluctuate considerably by age. In addition, the impact of assumptions used at very young ages on HLY estimates are seldom discussed, despite the fact that the majority of policies and initiatives at the EU level use HLY at birth, while data on health is only available after age 16. In this paper, we assess whether smoothing the age-specific prevalence distributions by different methods, extrapolating to older ages and changing assumptions at younger ages affect HLY estimates. Overall, assumptions made before age 15 are the most important and affect women and men differently, thus affecting HLY at birth for some countries. Estimates at age 65 are very slightly impacted. Generalised linear models (GAMs) seem promising for harmonising and extrapolating to older ages, while using polynomials or aggregating into 5-year age groups seem best for younger ages. As most EU policies use HLY at birth and by sex for developing and monitoring health policies, caution is needed when estimating HLY at birth.