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Frequent prescription of medication in an unapproved manner (off-label or unlicensed) in the neonatal setting is a result of the limited availability of adequately studied drugs in the pediatric population. Given that little information is available on this issue from eastern European countries, the purpose of this study was to describe for the first time the extent and pattern of off-label or unlicensed use of medicines in newborns in the Slovak Republic.Cross-sectional study was performed at the Department of Pathological Newborns of Children's University Hospital, Bratislava, and Unit of Pathological Newborns of Teaching Hospital Nitra. Data were collected on hospitalized neonates admitted between 1 April and 30 September 2012 who received pharmacotherapy. Label status of the administered drugs was determined according to the Slovak Summaries of Product Characteristics.A total of 962 prescriptions referring to 97 different medications was administered to 202 hospitalized newborns (46% premature). Anti-infectives and alimentary drugs were the most commonly prescribed. Of all prescriptions, 43% were identified as off-label and 4.8% as unlicensed. At least one off-label or unlicensed drug was given to 88.6% of patients. Ketoconazole was the most frequent drug used in an unapproved manner. A total of 13.8% of all prescriptions was administered despite contraindication.Administration of drugs to newborns in an unapproved manner was common in the participating Slovak neonatal wards, reflecting the lack of appropriate pediatric drug labeling.