Abstract Background When there is no authorized on- or in absence even no off-label treatment for patients with rare diseases, pharmacists have to compound medicinal products to meet the patients special needs. However it is important that there is evidence in the medical and/or pharmaceutical literature for such compounded medications. Position statement Pharmaceutical compounding must be performed in the best possible circumstances by certified practitioners (pharmacists) using validated standard operating procedures (standardized formulations) in order to obtain medicinal products of the highest quality to assure patient safety. More than 60 compounding procedures were identified in 17 on-line pharmaceutical compounding reference sources worldwide but more operating procedures still need to be validated. All ingredients used in the preparation of the compounded medication must be accompanied by a certificate of analysis and full records of the pharmaceutical production process need to be kept for full traceability and accountability.