In this paper, the utilities of the clearance concept-based pharmacokinetic analysis to study systemic disposition characteristics and targeting efficacy of various macromolecular drug carriers are demonstrated. The relationships between physicochemical and biological properties and uptake clearance values of macromolecules in various organs are discussed for designing a targeting system employing them. Based on the information about the effects of molecular size and electric charges on in vivo disposition of model macromolecules, the passive and active targeting system for an anticancer agent to a tumor is developed. Targeting efficacy of carrier systems utilizing carbohydrate-recognition mechanism were also quantitatively characterized in the same way. Thus, pharmacokinetic analysis was demonstrated to make a significant contribution in the rational design of a targeting system.