Objectives : This study was undertaken to examine the metabolomic changes due to gender and diurnal variation at sampling time and to identify an appropriate time point for urine sampling in epidemiologic studies using metabolomic profiles. Methods : Urine samples were collected twice a day (morning and afternoon) from 20 healthy Korean adults after fasting for 8 hours. The metabolomic assay was investigated using $^1H$ NMR spectroscopy coupled with the principal components analysis (PCA) and partial least squares discriminant analysis (PLS-DA). The metabolites responsible for differentiation between groups were identified through the loading plot of PLS-DA and quantified using Chenomx NMR Suite with a 600 MHz library. Results : Metabolites responsible for differentiation in gender and sampling time were creatinine, trimethyl anine oxide (TMAO), hippurate, mannitol, citrate and acetoacetate. Dimethylamine showed difference only as a factor of diurnal time. The level of creatinine was higher in men compared to women, and the levels of citrate, TMAO, hippurate, mannitol, and acetoacetate were higher in women compared to men. The levels of creatinine, TMAO, hippurate, dimethylamine and mannitol were higher in the morning rather than the afternoon while those of citrate and acetoacetate were higher in the afternoon rather than the morning. Conclusions : Since urinary metabolomic profiles varied by gender and diurnal cycle, urine sampling should be performed at the same time point for all participants in epidemiologic studies using metabolomic profiles.