Runs of homozygosity (ROH) are contiguous stretches of homozygous genome which likely reflect transmission from common ances- tors and can be used to track the inheritance of haplotypes of interest. In the present paper, ROH were extracted from 50K SNPs and used to detect regions of the genome associated with susceptibility to diseases in a population of 468 Holstein-Frisian cows. Diagnosed diseases were categorised as infectious diseases, metabolic syndromes, mastitis, reproductive diseases and locomotive disorders. ROH associated with infectious diseases, mastitis and locomotive disorders were found on BTA 12. A long region of homozygosity linked with metabolic syndromes, infectious and reproductive diseases was detected on BTA 15, disclosing complex relationships between immunity, metabolism and functional disorders. ROH associated with infectious and reproductive diseases, mastitis and metabolic syndromes were observed on chromosomes 3, 5, 7, 13 and 18. Previous studies reported QTLs for milk production traits on all of these regions, thus substantiating the known negative relationship between selection for milk production and health in dairy cattle.