Hepatobiliary transport mechanisms have been identified to play a significant role in determining the systemic clearance for a number of widely prescribed drugs and an increasing number of new molecular entities (NMEs). While determining the pharmacokinetics, drug transporters also regulate the target tissue exposure and play a key role in regulating the pharmacological and/or toxicological responses. Consequently, it is of great relevance in drug discovery and development to assess hepatic transporter activity in regard to pharmacokinetic and dose predictions and to evaluate pharmacokinetic variability associated with drug-drug interactions (DDIs) and genetic variants. Mechanistic predictions utilizing physiological-based pharmacokinetic modeling are increasingly used to evaluate transporter contribution and delineate the transporter-enzyme interplay on the basis of hypothesis-driven functional in vitro findings. Significant strides were made in the development of in vitro techniques to facilitate characterization of hepatobiliary transport. However, challenges exist in the quantitative in vitro-in vivo extrapolation of transporter kinetics due to the lack of information on absolute abundance of the transporter in both in vitro and in vivo situations, and/or differential function in the holistic in vitro reagents such as suspended and plated hepatocytes systems, and lack of complete mechanistic understanding of liver model structure. On the other hand, models to predict transporter-mediated DDIs range from basic models to mechanistic static and dynamic models. While basic models provide conservative estimates and are useful upfront in avoiding false negative predictions, mechanistic models integrate multiple victim and perpetrator drugs parameters and are expected to provide quantitative predictions. The aim of this paper is to review the current state of the model-based approaches to predict clinical pharmacokinetics and DDIs of drugs or NMEs that are substrates of hepatic transporters.