There are four Czech horse breeds: Silesian Noriker, Czech-Moravian Belgian, Old Kladruber (grey and black colour variety) and Hutsul included among the endangered breeds (Genetic Resources). These populations are currently closed to outside breeding. Effective population size is an important parameter used to assess genetic diversity for conservation program in these endangered breeds. Pedigree records for reference population, which included animals born in a 14-year period (from 1996 to 2010) were used for calculation. Realized effective population size was estimated from the individual rate in coancestry, from the individual increase in inbreeding and as effective population size based on population sex ratio. The values of effective population sizes were found low for all four analysed breeds. The results shown, that calculation based on population sex ratio gives overestimated values of effective population size. The approaches using either individual increase in inbreeding or individual increase in coancestry are more accurate and useful.