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The purpose of this study was to identify plasma metabolites associated with superior endurance running performance. In 2016, participants at the Western States Endurance Run (WSER), a 100-mile (161-km) foot race, underwent non-targeted metabolomic testing of their post-race plasma. Metabolites associated with faster finish times were identified. Based on these results, runners at the 2017 WSER underwent targeted metabolomics testing, including lipidomics and choline levels. The 2017 participants’ plasma metabolites were correlated with finish times and compared with non-athletic controls. In 2016, 427 known molecules were detected using non-targeted metabolomics. Four compounds, all phosphatidylcholines (PCs) were associated with finish time (False Discovery Rate (FDR) < 0.05). All were higher in faster finishers. In 2017, using targeted PC analysis, multiple PCs, measured pre- and post-race, were higher in faster finishers (FDR < 0.05). The majority of PCs was noted to be higher in runners (both pre- and post-race) than in controls (FDR < 0.05). Runners had higher choline levels pre-race compared to controls (p < 0.0001), but choline level did not differ significantly from controls post-race (p = 0.129). Choline levels decreased between the start and the finish of the race (p < 0.0001). Faster finishers had lower choline levels than slower finishers at the race finish (p = 0.028).