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The results of scientific research of the functional asymmetry of paired gonads of dairy cows had been studied. Statistical analysis of the lateral localization of morphofunctional ovarian state of cows during the different phases of the sexual cycle confirmed the conclusions of the evolutionary concept of the relevance of functional asymmetry of paired organs of bilateral organisms. The adaptive relevance is displayed by organizing the lateral structure on principle of enantiomeric domination. The quantitative ratio of the activity of the left or right ovaries in cows from different populations had been confirmed for the first time. According to our research, the abovementioned ratio was close to universal harmonic proportion of L/R as 1.000/1.612-1.622. We had revealed that environmental change impact the universal biological mechanism of self-regulation of functions in complex multicomponent living systems. The relative dominance of the right gonad in cows and the inversion phenomenon of dominance under the influence of hormonal stimulation of multiple folliculogenesis by the injection of gonadotropic drugs (FSH) had been proved for the first time. Experimentally established fundamental laws of the structural organization of the functional asymmetry of the of cows paired gonads allowed to the development of applied ways of improving the methods of stimulation and optimization of reproductive function of lactating dairy cows and donor- recipients of pre-implantation cattle embryos.