Runs Of Homozygosity (ROH) are a newly introduced approach for identifying inbreeding in diploid individuals. This approach is more reliable and available than pedigree data, but the lack of universal standards about ROH definition and identification introduces serious bias in ROH studies. In this thesis, ROH were analyzed in five cattle breeds (Brown Swiss, Fleckvieh, Norwegian Red, Pinzgauer and Tyrol Grey). The effects of SNP chip density and genotyping errors were tested on Brown Swiss, Pinzgauer and Tyrol Grey in order to establish the most optimal settings for precise estimation of levels of autozygosity. Data from the 50 k chip led to an overestimation of the number of ROH shorter than 4 Mb, since the analysis could not identify heterozygous SNPs present on the denser chip. Conversely, data from the denser chip underestimated the number of ROH longer than 8 Mb, unless the presence of a small number of heterozygous SNP genotypes was allowed within a ROH. Using this options ROH were identified in Brown Swiss, Fleckvieh, Norwegian Red and Tyrol Grey. Levels of autozygosity were calculated and compared with pedigree inbreeding coefficients. For all four breeds, population inbreeding levels estimated by the genomic inbreeding coefficients FROH > 8 Mb and FROH > 16 Mb were similar to the levels estimated from pedigrees. In contrast, inbreeding estimates based on FROH > 1 Mb and FROH > 2 Mb were considerably higher than pedigree-derived estimates. Pearson correlations between FROH and FPED ranged from 0.50 to 0.72, as dependent on pedigree depth. In the analysis of inbreeding depression a significant influence of FPED, FROH2 - 4 Mb and FROH > 2 Mb on total number of spermatozoa in 554 Fleckvieh bulls was found. Exact autozygous regions that influence this trait were detected on chromosomes 7, 10, 17, 20, 22 and 27 containing 41 genes. Five obvious candidate genes were found which are known to be directly associated with spermatogenesis, energy levels in spermatozoa and osmotic balance of the sperm. In conclusion, genotyping errors and SNP chip density do affect estimates of autozygosity from ROH, ROH distributions (number and size) enables precise estimation of autozygosity at individual and population levels in cattle and genomic autozygosity does have influence on bull semen quality.