Background : Most human metabolomics studies have shown that spectral outputs of 1 H nuclear magnetic resonance fingerprinting are strongly influenced by inter- and intra-individual variations; however, few studies have been performed to evaluate the inter- and intra-individual variations in urinary endogenous metabolites. Methods : We recruited 30 male college students to evaluate the factors affecting intra- and inter-individual variations in urinary endogenous metabolites. Statistical analysis for variations in urinary metabolites was performed after eliminating outliers found in principal component analysis (PCA) plots. Results : Inter-individual variations were relatively low for 2-oxoglutarate, succinate, citrate, dimethylglycine, and taurine, but high for trimethylaminoxide (TMAO), hippurate, and lactate. Intra-individual variations for 2-oxoglutarate, citrate, dimethylglycine, and taurine were relatively low, but high for TMAO and hippurate. The factors affecting inter-individual variation of lactate were age, body mass index, beverages, and alcohol, whereas the factors affecting intra-individual variation of lactate were age and fish. Kim Chi intake affected the inter-individual variation of succinate, citrate, TMAO, and hippurate; however, it did not affect the intra-individual variation of endogenous metabolites. Conclusions : Our results showed that inter- and intra-individual variations in urinary endogenous metabolites were very large, and significant factors affecting inter- and intra-individual variation were diverse, even after eliminating outliers in PCA analysis. Clin Chem Lab Med 2009;47:188–94.