Interest in bile acids (BAs) is growing due to their emerging role as signaling molecules and their association with various diseases such as colon cancer and metabolic syndrome. Analyzing BAs requires chromatographic separation of isomers, often with long run times, which hinders BA analysis in large studies. Here, we present a high-throughput method based on liquid chromatography-tandem mass spectrometry to quantify BAs in mouse samples. After acidic protein precipitation in the presence of a comprehensive mixture of stable isotope-labeled internal standards (SIL-ISs), BAs are separated on a biphenyl column by gradient elution at basic pH. Quantification is performed using a six-point calibration curve. Except for the separation of β- and ω-muricholic acid (MCA) species, a rapid separation of 27 BA species was achieved in a run time of 6.5 min. Plasma quality controls (QCs) were used to evaluate intra- and inter-day precision. The CV was less than 10% for most BA species and exceeded 20% only for glycohyodeoxycholic (GHDCA) and taurohyodeoxycholic acid (THDCA) due to the lack of a corresponding SIL-IS. The limit of quantification (LoQ) was tested using diluted QCs and was found to be compromised for some BA species as a result of insufficient isotopic purity of the SIL-IS, leading to significant interference with the respective analyte. Finally, we tested the mouse sample material requirements for plasma, bile, and liver samples and determined BA concentrations in C57/BL6N wild-type mice. In conclusion, the LC–MS/MS method presented here permits a rapid and reproducible quantification of the major murine BAs.