Background Late presentation (LP), defined as a CD4 count < 350/mm3 or an AIDS-event at HIV-diagnosis, remains a significant problem across Europe. Linking cohort and surveillance data, we assessed the country-specific burden of LP during 2010–2016 and the occurrence of new AIDS events or deaths within 12 months of HIV-diagnosis believed to be attributable to LP. Methods Country-specific percentages of LP and AIDS-events/death rates (assessed with Poisson regression) observed in The Collaboration of Observational HIV Epidemiological Research Europe (COHERE) and EuroSIDA cohorts, were applied to new HIV-diagnoses reported to the European Centre for Disease Prevention and Control. The estimated number of LP in the whole population was then calculated, as was the number of excess AIDS-events/deaths in the first 12 months following HIV-diagnosis assumed to be attributable to LP (difference in estimated events between LP and non-LP). Results Thirty-nine thousand two hundred four persons were included from the COHERE and EuroSIDA cohorts, of whom 18,967 (48.4%; 95% Confidence Interval [CI] 47.9–48.9) were classified as LP, ranging from 36.9% in Estonia (95%CI 25.2–48.7) and Ukraine (95%CI 30.0–43.8) to 64.2% in Poland (95%CI 57.2–71.3). We estimated a total of > 320,000 LP and 12,050 new AIDS-events/deaths attributable to LP during 2010–2016, with the highest estimated numbers of LP and excess AIDS-events/deaths in Eastern Europe. Country-level estimates of excess events ranged from 17 AIDS-events/deaths (95%CI 0–533) in Denmark to 10,357 (95%CI 7768-147,448) in Russia. Conclusions Across countries in Europe, the burden of LP was high, with the highest estimated number of LP and excess AIDS-events/deaths being in Eastern Europe. Effective strategies are needed to reduce LP and the attributable morbidity and mortality that could be potentially avoided.