The purpose of this study was to analyze the morpho-functional features of the ovaries and uterus of sows with different genotypes for the estrogen receptor (ESR), prolactin receptor (PRLR), and follicle-stimulating hormone subunit beta (FSHβ) genes associated with reproductive traits. Healthy Large White sows were studied. The genotypic status of the ESR, PRLR, and FSHβ genes was detected by polymerase chain reaction-restriction fragment length polymorphism. The structure of the ovaries and uterus was studied using quantitative assessment of organs and histological research. Sows with the ESR BB genotype significantly exceeded animals with the ESR AA genotype in milk yield (by 0.3 kg) and in the number of piglets at birth (by 0.9 animals) and at weaning (by 0.7 animals). Sows with the ESR AB genotype were midway between those with ESR BB and ESR AA genotypes in terms of these reproductive traits. Animals with the PRLR AA genotype significantly exceeded those with the PRLR BB genotype in the number of piglets born (P < 0.05); the differences in litter weight at birth were not significant. Compared to other genotypes, sows with genotypes ESR BB (P < 0.05) and PRLR AA (AB) (P < 0.05) had larger uteruses and more yellow bodies, tertiary follicles, and primordial follicles in their ovaries. Animals with the FSHβ BB genotype significantly exceeded animals with the FSHβ AB genotype in the length of uterus by 21 cm (P < 0.05).