Due to their activity against bacteria, viruses, and fungi, antimicrobial peptides are important factors in the innate resistance system of humans and animals. They are called "new generation antibiotics" for their potential use in preventive and therapeutic medicine. The most numerous group of antimicrobial peptides is a family of cationic peptides which include defensins and cathelicidins. Among them the most common are peptides with a beta-sheet structure containing three intra-molecular disulphide bonds, called defensins, comprising three classes: alpha, beta, and theta. The class of beta-defensins is the largest one. Their transcripts have been found in many tissues of humans and animals. The aim of this paper is to present the current knowledge about antimicrobial peptides from the defensin family in farm animals, their expression, polymorphism, as well as the potential of their use as genetic markers of health and production traits.