The aim of this work was to verify the efficacy of 12 horse microsatellite markers (AHT4, AHT5, ASB2, HMS2, HMS3, HMS6, HMS7, HTG4, HTG6, HTG7, HTG10 and VHL20) in parentage control of Silesian horses and Thoroughbreds. The allele identification was performed using automated DNA sizing technology. The effective number of alleles, polymorphism information content (PIC) and probability of exclusion (PE) were estimated. According to the calculated coefficients, the most valuable markers for testing were ASB2 in the Silesian horses and Thoroughbreds and HMS2 in Silesian horses. The probability of exclusion when using only 6 polymorphic loci in Silesian and Thoroughbred horses exceeded 0.99 and increased to 0.999 when all the loci tested were taken under consideration. The obtained results confirm the efficacy of the investigated microsatellite panel for parentage testing among Silesian horses and Thoroughbreds.