An increased knowledge of endocrine systems during incubation not only results in a better understanding of fundamental aspects of embryonic development, but also may lead to new practical applications. A first and immediate aspect is the possibility of early sex diagnosis based on current knowledge of sex determination. The current practice of killing day-old male chicks of layers results essentially from the improved efficiency of modern egg and meat lines, which were selected in opposite directions. The disposal of unwanted male chicks from layer lines causes increased welfare and ethical concern. Therefore, attempts have been made to interfere with sex determination or to identify the unwanted gender of the embryo at a certain stage of development (e.g. based on endocrine differences) where public concern is no longer a point of resistance against elimination. Thyroid hormones as well as glucocorticoids are known to be involved in several events leading to hatch and in the quality of the hatchling. Both seem to be strongly influenced by a common hypothalamic factor in the late chick embryo: corticotrophin-releasing hormone (CRH), CRH-related urocortines or analogues for CRH-receptor activity may be combined with in ovo vaccination for stimulating or synchronizing hatching activity. A next question to be asked is whether incubation conditions that produce the best hatchability also automatically result in chicks of the highest quality with the best desired postnatal performance. During prenatal development, most of the functional systems develop from an open loop system without feedback into a closed control system with feedback. This is already documented for endocrine systems such as the thyroid, the corticotroph and the gonadal axis. For functional systems, critical periods seem to exist and it is presumed that these coincide with the transition from an open into a closed feedback control system. In consequence, variation in incubation conditions such as temperature may induce a lifelong determination of physiological control systems, most probably via long-term changes in the expression of related effector genes and this may be defined as epigenetic adaptation. This opens possibilities to improve incubation conditions, not only in view of hatchability/chick quality but also taking long-term effects into account. Also it may redirect, at least to some extent, development as a function of the aims set forward, e.g. metabolic conditioning.