We analyze markers of carnitine insufficiency and deficiency, lysine (LYS) and methionine (MET), in 39 neonates with intrapartum hypoxia (selection criteria: umbilical artery pH <7.20, lactate >1.8 mmol/l and PaO2 <25 mm Hg), and in 35 healthy newborn infants (control group) in the early neonatal period (1-7 days of life). Free (FC), total (TC) carnitine and acylcarnitines (AC=short-chain+long-chain acylcarnitines) were measured using a radioisotopic micromethod; LYS and MET were determined by high-pressure liquid chromatography. AC and TC plasma concentrations and AC/FC ratio were higher while FC/TC ratio was lower in the hypoxic neonates than in the control group. Hypoxic newborn infants (59%) presented "carnitine deficiency" (FC/TC <0.7) and 60% of them "carnitine insufficiency" (AC/FC ratio >0.4) vs. 31% and 28%, respectively, for the neonates of the control group (p<0.05). In the healthy neonates group, MET correlated with FC/TC and the AC/FC ratio. FC, TC, AC, AC/FC and umbilical artery pH (pHua) were inversely correlated. FC/TC and MET correlated with pHua. We conclude that: (1) an important percentage of newborn infants with intrapartum hypoxia suffer carnitine deficiency and carnitine insufficiency in the early neonatal period, related to MET plasma levels; (2) the carnitine deficiency or insufficiency in the neonate is determined by the degree of intrapartum acidosis.