In this study, stirred yoghurts were produced from Turkish Holstein cow milk with different genotype combinations of beta-lactoglobulin and beta-casein. The distribution of AA, AB, and BB genotypes of beta-lactoglobulin and A1A1, A1A2, and A2A2 genotypes of beta-casein was determined in a total of 135 cow milk samples. Raw cow milk samples containing AA genotype of beta-LG exhibited higher non-fat total solids, protein, and fat contents in comparison to milk containing AB and BB genotypes of beta-LG. Compared to the samples made from milk with other beta-LG genotypes, the stirred yoghurt made from milk with beta-LG AA genotype showed lower degree of syneresis and higher for hardness, apparent viscosity, and consistency coefficient. The lowest number of grains, the perimeter of grains, and the visual roughness values were obtained in the stirred yoghurts made from milk with BB genotype of beta-LG and A2A2 genotype of beta-CN. The sensory analysis revealed that beta-CN genotypes of milk significantly influenced the overall acceptability scores of the stirred yoghurts, while beta-LG genotypes did not significantly influence these scores except for the visual grainy score. The findings of this study showed that the selection of specific milk protein genotypes resulted in substantial differences in the physicochemical and sensory properties of stirred yoghurt.