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The pathogenesis and progression of hypoxic-ischemic encephalopathy (HIE), a major cause of severe neurological disability and mortality in the perinatal period, are shaped by the interplay of multiple processes, including inflammation, oxidative stress, and excitotoxicity. We conducted a longitudinal study to determine biomarkers of oxidative stress and inflammation in noninvasive urine samples of newborns with moderate/severe HIE ( N  = 51), employing liquid chromatography-mass spectrometry. We noted that levels of several biomarkers of oxidative stress increased over time, demonstrating the ongoing propagation of oxidative injury. Prostaglandins, in contrast, showed a decreasing trend in their concentration profiles over time, which probably reflects their mediation in pathogenic mechanisms, including the inflammatory response. Statistically significant differences in the levels of oxidative stress of neonates with distinct brain lesion patterns, as detected with magnetic resonance imaging (MRI), were observed, revealing an increase of lipid peroxidation biomarkers in newborns with cerebral lesions (MRI score of 1 compared with scores of 0 and 2). Moreover, a gender-dependent study showed no statistically significant differences in biomarker concentrations between male and female infants. Our observation leads to the hypothesis that monitoring of noninvasive lipid peroxidation biomarkers could aid in diagnosis and prediction of long-term outcomes as a complementary tool to standard exploration. Antioxid. Redox Signal. 35, 1467-1475.