Intensive genetic selection of swine, which took place during last 15 years, tended to gain highest productivity, including fertility, reproductive performance, feed conversion and dynamic increase of body weight. This selection resulted in significantly higher production and financial effects that overpass traditional production systems. The new genetic approach however, generated also some unwanted results, which are cited in this paper. One of them is the lean phenotype of swine which is characterized by higher susceptibility to infectious diseases. This depends upon the animals low resistance to chronic stress, development of immunosuppression and increased risk of infection due to the decreased innate immunity. Here, the major infectious agents, presenting threats for those herds, were presented. Since the facultatively pathogenic organisms dominate, the improvement of animals welfare and immunoprophylactic measurements are strongly recommended. Treatment with antimicrobials should be restricted to “the prudent use” principle. The crucial role of host microbiota, residing in the same environment and preventing pathogens colonization, was underlined. Also swine production and losses in the intensive farming systems in Italy and Poland were compared.