The linkage point between kinetics and dynamics of drugs and other foreign chemicals is at the active site of the target. The response is determined within certain limits by the concentration of the substance at the target and its mechanism of action. However, the concentration of the substance at the active site under in vivo conditions cannot be easily measured, and surrogates such as plasma concentration are used instead. The emergence of in vitro approaches to study some primary pharmacokinetic (PK) and pharmacodynamic (PD) processes in simpler experimental setups could provide ways to estimate the concentration at the active site, which then can be used in a more reliable extrapolation and prediction of in vivo behavior and action of the substance. Imaging and other novel analytical techniques are providing direct or indirect measurements of in vivo concentrations in tissues. In this review, processes such as transport, metabolism, etc. affecting the concentration of the substance at the active site are discussed, analytical possibilities to measure directly or estimate indirectly the concentration at the active site are illustrated, the overall design and performance of physiologically based PK-PD models are described, and some examples concerning blood-brain barrier, liver, and lungs are presented. In conclusion, several important recommendations are made: (1) In vitro systems should be characterized in a much more detailed way than has been done so far, especially with respect to unbound concentrations at the sites of disposition and action; (2) kinetics of the compound in the in vitro system have to be more thoroughly characterized; (3) local models encompassing the in vitro system should be developed and used; and (4) PBPK/PD models should incorporate these local models.