Although genomic selection based on genotyping arrays is a prevailing approach to breeding in farm species, weak points of this technology can be detected. Despite the additional inclusion of the data from functional genomics, negative co-selection in health and reproduction traits has been stated. Adding of particular genes linked to these traits to genetic evaluation can reduce the negative trends. In this context, screening for the diversity of genes associated with innate immunity is carried out in the Czech Red Pied cattle population. Evaluation of the found gene variants in association studies demonstrated not only the effect on health traits but also a pronounced effect on the female reproductive traits in the case of the tested TLR genes from the anti-bacterial series. This data complements the published effect of these primarily immune genes on the reproductive traits in model species like mice and humans. Additional genes with the breeding potential are MYD88 and two genes coding for the subunits of the transcription factor NFkappaB. Particularly, their effect on resilience in physiological traits should be tested.