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Medicines used in neonates contain different excipients, which may not be safe in this age group.To analyse the frequency at which hospitalised neonates are exposed to harmful excipients (HEs) and to identify substitution possibilities for medicines containing HEs.Retrospective, observational study at a university paediatric hospital from 1 September 2015 till 29 February 2016. All hospitalised neonates who received a prescription for medicines containing an HE were included. Neonates were divided into four groups according to gestational age (<28 weeks; 28 to <32 weeks; 32 to <37 weeks and ≥37 weeks). The following excipients were analysed: parabens, polysorbate 80, propylene glycol, benzoates, saccharin sodium, sorbitol, ethanol and benzalkonium chloride. Excipients were identified from the Summaries of Product Characteristics.296 (102(34.5%) preterm) neonates included in the study received 1472 prescriptions for 106 medicines. The most often used formulations were intravenous (48/106; 45.3%) and oral solid formulations (20; 18.9%). The total number of different excipients was 169. In total, 29/106 (27.4%) medicines contained at least one HE. In total 82/102 (80.4%) preterm and 118/194 (60.8%) term neonates received medications with at least one HE. Substitution was possible for 9/29 (31.0%) HE-containing medicines.Use of HEs can be reduced by using HE-free products available on the European market. However, medicine substitution was possible in only a small number of cases. Therefore the main focus should be on information and education of the hospital specialists about HEs used in medicines and their adverse reactions.