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The genetic structure of five goat breeds bred in Slovakia was characterized using a visible genetic profile and biochemical polymorphic systems. Tree dairy goat breeds – White Shorthaired, Brown Shorthaired and Alpine goats – and two wool goat breeds – Angora and Cashmere goats – were evaluated. Calculated were the heterozygosity and the effective number of alleles for each locus based on the allele frequencies of eight genes determining type traits and biochemical polymorphic systems, as well as their average values as indicators characterizing the genetic variability of each breed. The genetic differences between breeds were also determined.