Endogenous substances in the body are controlled through simple, very effective mechanisms, that preserve an optimum homeostatic equilibrium of baseline concentration and restore it when impaired. When planning a pharmacokinetic investigation of an endogenous substance exogenously administered, it is imperative to carefully ascertain the above mechanisms as well as the baseline value and their possible variations associated with daily rhythm, food, age, sex, menstrual cycle. Often the control mechanisms operate through non-linear processes, therefore a non-compartmental analysis or a tailored model may be more appropriate than the compartmental models used in standard pharmacokinetic analysis. Some specific examples of endogenous substances are discussed here on the basis of the data from the literature and personal experience.