Medication errors are probably more common in neonates than is generally appreciated. In Mexican pediatric hospitals, L-carnitine is mainly used for nutritional support and to treat cardiomyopathy secondary to neonatal asphyxia. Using a longitudinal-retrospective approach we assessed the appropriateness of all L-carnitine prescriptions written during a 12-month period at a NICU of a second-level hospital located in Toluca, Mexico. Reports of adverse reactions possibly related to L-carnitine therapy were collected and characterized. Overall, administration of L-carnitine was considered justified and appropriate only in 18% of patients. 60.7% of L-carnitine prescriptions were rated as inappropriate because the prescribed doses fell outside the recommendations. The overall rate of ADRs calculated from the patient population was 18.03%. All of them were of gastrointestinal type: abdominal cramps (8 cases, 61.54%) and vomiting (5 cases, 38.46%). Our results supported the establishment of an L-carnitine rational use policy at the NICU of the hospital under study.