Studies in the field of molecular nutrition and food research often aim at identifying effects of bioactive ingredients on living organisms. When data from human studies are difficult to obtain, effects are often studied in relevant animal or cellular in vitro models. This poses the need for adequate extrapolation from the in vitro to the in vivo situation, from high-dose levels to realistic low-dose levels and from experimental animals to humans. Furthermore, effects of genetic polymorphisms or lifestyle factors may have to be taken into account. Physiologically based kinetic (PBK) modeling provides a means to support these kinds of extrapolations. The present paper illustrates the basic concepts of PBK modeling. PBK modeling includes six steps: (i) definition of the conceptual model, (ii) translation into a mathematical model, (iii) defining parameter values, (iv) solving the equations, (v) evaluation of model performance and (vi) making predictions. The paper provides an overview of these basic steps and presents examples to illustrate how PBK modeling can be applied. This reveals that PBK modeling provides an important tool in the field of the 3Rs aiming at Replacement, Reduction and Refinement of animal studies and may also be a useful tool for risk assessment.