Three draught horse breeds are maintained in the Czech Republic: the Silesian Noriker (SN), the Noriker (N), and the Czech-Moravian Belgian (CMB). Because the SN and CMB populations are currently closed to outside breeding and are endangered (Genetic Resources), the loss of the genetic variation these horses represent is concerning. Genetic diversity within and between these three breeds and their population structures was analyzed based on pedigree information. Our goal was to identify and quantify factors that affected their genetic variability. The effective population size was analyzed in each breed. The numbers of generations were 22, 32, and 32 for the SN, N, and CMB breeds, respectively, with average equivalent known generations of 9.81, 8.45, and 8.91, respectively. The effective numbers of founders and ancestors contributing to the current genetic pool were, respectively, 69.42 and 22.32 for the SN breed, 98.48 and 42.20 for the N breed, and 43.33 and 23.32 for the CMB breed. The average inbreeding coefficients were 4.6%, 2%, and 4% for the SN, N, and CMB breeds, respectively, and the average inbreeding rate was 0.5% for the SN and CMB breeds and 0.2% for the N breed. The corresponding estimates of effective population size were 95, 195, and 101 for the SN, N, and CMB breeds, respectively. These statistics suggest that the genetic variability has decreased, and without changes in breeding strategy the genetic variability might continue to decline. Using genealogical F-statistics, small genetic differences were identified between the analyzed populations (FST = 0.02).