Conservation of genetic variability within a breed is the core problem of the conservation of rare breeds of domestic livestock species. The objective of our study was to examine the genetic differences and genetic variation of the large-type Žemaitukai horse population. The main study was conducted in 1996–2005 at the Institute of Animal Science of Lithuanian Veterinary Academy. The pedigree, gene frequencies of blood group and serum protein markers, homozygosity, and genetic similarities were analysed from 138 horses. The genetic analysis of alleles indicated that the Al^AB genotype was dominant in large-type Žemaitukai, the genotypes Tf^FF, ^FO being also frequent. The alleles D^dghm, D^cgm, D^dk, D^dl in blood group system were also frequent. The frequency of alleles D^dk and Es^II of Kalmanas line was its distinguishing feature. The average homozygosity was 33.41% in the large-type Žemaitukai horse population. The number of effective population size for large-type Žemaitukai is 58; the survival of the population is uncertain.

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