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The amniotic and allantoic fluid compartments in the mare serve essential roles throughout pregnancy and parturition. Although the global metabolomic profile of amniotic fluid in women has been extensively characterized, current data for equine fetal fluids are limited. Therefore, the goal of this study was to characterize the global metabolomic profile of equine allantoic and amniotic fluid through nuclear magnetic resonance spectroscopy. Fetal fluids were collected between 270 and 295 days of gestation from 12 pregnancies through ultrasound-guided transabdominal puncture. A total of 24 samples (n = 10 allantoic fluid; n = 9 amniotic fluid; n = 5 admixed fluid) were analyzed by one-dimensional proton (1H) and two-dimensional (1H-13 C) nuclear magnetic resonance spectroscopy. Metabolites were integrated and compared between fluid types using a Kruskal–Wallis test at P <.05 significance. A total of 28 distinct metabolites were found in allantoic and admixed fluid, whereas 23 metabolites were identified in amniotic fluid. Allantoic fluid contained significant elevations (P <.05) in the metabolites betaine, creatine, creatinine, citrate, histidine, nitrophenol, tryptophan, π-methylhistidine, and unknown metabolite #1 compared with amniotic fluid, whereas amniotic fluid contained statistically increased concentrations of the metabolite lactate compared with allantoic fluid (P =.003). • We describe the global metabolomic profile of equine allantoic and amniotic fluid. • Twenty-eight distinct metabolites were found in allantoic and admixed fluid. • Twenty-three distinct metabolites were found in amniotic fluid. • These profiles may serve for future studies of gestational abnormalities. [ABSTRACT FROM AUTHOR]