Marketing authorisation of orphan medicines in Europe from 2000 to 2013

•Analysis on 157 orphan designated medicines at EU marketing authorisation (MA).•Company size is a determinant for MA success.•Compliance with scientific advice is a determinant for MA success.•Scientific advice is a tool to optimise development towards MA success An analysis was performed on a data set of 157 orphan designated medicines with an outcome for marketing authorisation application (MAA) between 2000 and 2013. The intention was to understand the factors associated with marketing authorisation success, the challenges developers face regarding orphan medicine development, and how scientific advice (SA) is used during development. The results demonstrated that orphan medicines have a lower success rate compared with non-orphan medicines and that determinants for marketing authorisation success were company size and compliance with SA. Compliance with SA could help orphan medicine developers overcome clinical development challenges.