To select early, sensitive biomarkers of 3-chloro-1,2-propanediol (3-MCPD) exposure, a single dose of 30 mg/kg/day 3-MCPD was administered to male Wistar rats for 40 days. Significant elevations of serum creatinine and blood urea nitrogen concentrations were observed on day 40, and urine N-acetyl-beta-D-glucosaminidase and beta-galactosidase (beta-Gal) activities were observed on day 20. Slight renal tubule hydropic degeneration and spermatozoa decreases were observed on day 10. The endogenous metabolite profile of rat urine was investigated by ultra performance liquid chromatography/mass spectrometry with electrospray ionization (ESI). Principal component analysis and partial least-squares enabled clusters to be visualized, with a trend of clustering on day 10 in ESI- and the greatest differences on days 30 and 40. Galactosylglycerol, a marker contributing to the clusters, which had earlier variations than conventional biomarkers and the most significant elevations as compared to other novel biomarkers, was first considered to be an early, sensitive biomarker in evaluating the effect of 3-MCPD exposure. The identification of galactosylglycerol was carried out by beta-Gal catalysis, and the possible mechanism of urine galactosylglycerol variation was elucidated.