Background: The first estimates of Healthy Life Years at age 50 (HLY50) across the EU25 countries in 2005 showed substantial variation in healthy ageing. We investigate whether factors contributing to HLY50 inequalities have changed between 2005 and 2010. Methods: HLY50 for each country and year were calculated using Sullivan's method, applying the age-specific prevalence of activity limitation from the European Union Statistics on Income and Living Conditions (EU-SILC) survey to life tables. Inequalities in life expectancy at age 50 (LE50) and HLY50 between countries were defined as the difference between the maximum and minimum LE50 or HLY50. Relationships between HLY50 and macro-level socio-economic indicators were investigated using meta-regression. Men and women were analysed separately. Results: Between 2005 and 2010 HLY50 inequalities for both men and women in Europe increased. In 2005 and 2010 HLY50 inequalities exceeded LE50 inequalities, particularly in the established EU15 countries in 2010 where HLY50 inequalities (men: 10.7 years; women: 12.5 years) were four times greater for men and three times for women than LE50 inequalities (men: 2.4 years; women: 4.1 years). Only material deprivation significantly explained variation in EU25 HLY50 in both years with, additionally, long-term unemployment in 2010. Conclusions: Our results suggest that inequalities in HLY50 across Europe are large, increasing and partly explained by levels of material deprivation. Moreover long-term unemployment has become more influential in explaining variation in HLY50 between 2005 and 2010.