Nanomaterials have been found increasing applications in the food sector. Nanostructured antimicrobials can be incorporated either to food matrix of food packaging or to provide extended safety and quality. However, the interactions and effects of nanomaterials with biological systems are still poorly understood. Nanoparticles can enter the organism by oral, dermal and inhalation routes and distributed to different tissues by the circulatory system. Increasing evidence indicate that targeting to specific tissues, cellular uptake and intracellular fate of nanoparticles are strongly influenced by size, shape and surface properties. The specific characteristics of nanomaterials are also determinant for their toxicity in higher organisms. The dose, exposure time and administration route are important aspects influencing toxicity of nanoparticles as well. Both in vitro and in vivo evaluation studies on different types of nanostructures have providing information to support a better understanding about the interactions of nanoscale materials with biological systems.