Chimeric mice with humanized liver that are repopulated with human hepatocytes are useful to study hepatitis B and C viruses, predict drug metabolism and pharmacokinetics (PK), and evaluate hepatotoxicity. Understanding the characteristics of chimeric mice is important for making predictions in humans. In general, chimeric mice with more than 70% of replacement indexes (RIs), a value representing the occupancy ratio of the region of the human liver to that of the mouse liver, are used. However, chimeric mice with RIs less than 70% are also useful in understanding the species differences between mice and humans. In this study, to elucidate the effects of proliferating human hepatocytes and remaining mouse hepatocytes on bile acid concentrations in detail, we investigated the differences in the total concentrations of bile acids and their compositions in chimeric mice with different RIs. The total concentrations of bile acids in their sera increased as the RIs increased. The ratios of primary to secondary bile acids, percentages of glycine conjugates, and hydrophobicity indexes, obtained upon classifying bile acids based on their compositions in the serum and comparing them with those in normal mice and humans, were found to approach the values observed in humans as the RIs increased. The percentages of taurine conjugates were high in chimeric mice with high RIs, although their values were close to those in humans. These results could be fundamental in providing knowledge to accurately predict human PK and toxicity in chimeric mice with humanized liver.