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Abstract Several estimates of the lesser spotted eagle breeding population in Slovakia were published in 1955-2002. In this study we estimate the breeding population of the lesser spotted eagle by 1997 and 2014. By 1997, the estimated size of the breeding population was 762 pairs. In 2002 an estimate of the population size by 2000 was published at 800-900 pairs. By 2014 we estimate the breeding population of the lesser spotted eagle in Slovakia at 600-800 pairs and the declining population trend in 2000-2013 at -23%. Our estimate is supported by the extrapolation from data obtained in 2011-2013 in eight selected Special Protection Areas (SPAs) within a framework of the project LIFE09 NAT/SK/000396 “Conservation of Aquila pomarina in Slovakia”. When analyzing abundance, density and trends in the species’ entire breeding range in Slovakia we first summarised the numbers of breeding pairs, their densities and trends within the selected SPAs and then explored the differences among them using ANOVA and cluster analysis. For the eight SPAs as a whole (n = 8) or partitioned by a grid of the Databank of Slovak Fauna (n = 119 squares) we calculated the interval estimates of the mean number of pairs (unweighted and weighted arithmetic means and medians). By summarising these estimates and extrapolating to the species’ entire breeding range in Slovakia (c. 28,935 km2) while increasing the sample size (n = 8, 9, 11 and 1 2 SPAs), the size estimates stabilise at a level of 670 (mean with 95%LCL = 507 and 95%UCL = 834) or 765 (median with 95%LCL = 393 and 95%UCL = 841 ) breeding pairs. The most reliable estimate of the breeding population of the lesser spotted eagle in Slovakia by 2014 is a median of 765 pairs with a 95% confidence interval from 393 to 841 pairs and an interquartile range from 418 to 835 pairs. We estimate a 23% decrease in the breeding population during 2000-2013, i.e. a small decrease -1 (20-49%). Three methods of estimating were used: 1 ) comparing the numbers of pairs in the selected SPAs between 2000 and 2014 - indicates a decrease of -26%; 2) comparing the numbers of pairs from long-term monitoring in five areas (orographic units Vihorlatské vrchy Mts, Laborecká vrchovina Upland, Volovské vrchy Mts, Orava and Horné Ponitrie Regions) by the 1990s and 2014 - indicates a decrease of -20%; 3) comparing the numbers of pairs by 1997 in selected areas within the boundaries of the current SPAs with the number of pairs in the same SPAs by 2014 - indicates a decrease of -23%. In the eight selected SPAs the estimated decline was even more pronounced, reaching a median trend of -35% in the 95% confidence interval from -54% to +25%. The estimate by 1997 fits in with an increasing trend of published breeding population estimates in Slovakia during 1955-2002. The estimate by 2014 is lower than the estimate by 2000, and for the first time ever a declining trend is recorded. By 2014 the breeding grounds of the lesser spotted eagle in Slovakia embrace an area of c. 28,935 km 2 . Taking an estimate of 600-800 breeding pairs, the mean density varies between 2.1-2.8 pairs.100 km -2 .