The aim of this study was to evaluate the level of genomic inbreeding and effective population size in the Slovak Pinzgau population based on molecular – genetic analysis. The genotyping data was obtained from in total 152 animals (37 sires, and 115 cows) representing the active Pinzgau population in Slovakia. All of animals have been genotyped using Illumina BovineSNP50 BeadChip V2 and after quality control the final dataset was composed of 41,738 autosomal loci. The inbreeding coefficient (F_ROH) was expressed as the length of the genome covered by runs of homozygosity (ROH) divided by length of the autosomal genome covered by all SNPs (2.5 Gb). Across both groups of sires and cows ROH segments greater than 4 Mb (F_{ROH > 4 Mb}) cover in average 2.22 % of the genome, whereas inbreeding estimates > 16 Mb (F_{ROH > 16 Mb}) achieved 0.81 % that signalized recent inbreeding in analysed population. The historical and recent effective population sizes were estimated based on the relationship between the extent of linkage disequilibrium and effective population size. The estimates of historical effective population size showed linear decrease within each of analysed group. A decrease of 7.81 individuals per generation has been observed. The predicted current N_e across all of animals (30.29) clearly confirmed the endangered status of Slovak Pinzgau population and indicated the need for constant monitoring to increase population size without reduction of genetic diversity due to inbreeding.