The human intestine is said to harbor over 100 species of bacteria with a total of approximately 100 trillion bacterial cells. Studies in recent years have revealed that intestinal bacteria may be beneficiary to the host by contributing to health preservation and promotion. This has raised the attention on researches regarding the intestinal microbiota. In studying the effects that the intestinal microbiota has on its host, it is considered that the metabolites that the microbiota produces also play a role. This article introduces a method for the comprehensive measurement of the primary metabolites in mouse feces using GC-MS/MS and LC-MS/MS.