Atazanavir has been reported to increase total serum bilirubin level up to ninefold. It is widely believed that the observed total bilirubin elevation is primarily due to UGT1A1 inhibition. However, UGT enzymes are well-known as a low-affinity and high-capacity system, and the observed drug-drug interaction mediated by UGTs is usually less than twofold. There were discrepancies in the explanation of total bilirubin elevation due to UGT1A1 inhibition alone, suggesting the contribution of other mechanism(s) to the interaction. As atazanavir is a potent OATP1B1/3 inhibitor and the hepatic uptake of both unconjugated and conjugated bilirubin are mediated by OATP1B1/3, these transporters could be involved in the bilirubin-atazanavir interaction. To better understand the roles of UGT1A1 and OATP1B1/3 in this interaction, it would be useful to characterize the contribution of each individual pathway to the interaction. As multiple compounds, pathways, and potentially UGT1A1 polymorphism are involved, a thorough physiologically-based pharmacokinetic (PBPK) analysis was utilized to integrate the information from various relevant in vitro and clinical studies to quantitatively estimate the contribution of UGT1A1 and OATP1B1/3 inhibition to the interaction between bilirubin and atazanavir. The PBPK analysis indicated that UGT1A1 inhibition plays a modest role in bilirubin and atazanavir interaction contributing less than 33%. The results also suggested that unconjugated bilirubin is less sensitive than raltegravir upon UGT1A1 inhibition, therefore, unconjugated bilirubin may not be a useful endogenous biomarker for UGT1A1 inhibition. The analysis demonstrated that the metabolism of unconjugated bilirubin shares common features of other UGT enzyme-mediated reactions.