Selection for economic phenotypic traits has significantly improved poultry productivity over the past 70 years. However, there have been a number of undesirable changes in the regulation of energy homeostasis, fat deposition (mainly in breeders), increased sensitivity to high environmental temperature and intensified incidence of metabolic disorders. Gene expression can be modulated by environmentally (diet)-induced epigenetic changes that may affect the phenotypic traits in offspring. Increasing number of studies showed that information acquired from environmental (diet) exposure may be transmitted across generations. This chapter focuses on nutritional programming and transgenerational epigenetic inheritance in birds as well as the potential role of nutrigenomics in poultry breeding and selection. The chapter identifies the challenges which may help in understanding the avian epigenome and improve, in turn, the genetic selection of super parent stocks.