Small and medium-sized enterprises (SMEs) are an important source of innovative medicines. Compared with their larger counterparts, they experience challenges as a result of insufficient human and financial resources that can hamper drug development and regulatory compliance. This analysis reviews the profile of major objections raised in marketing authorisation applications for medicines for human use submitted by SMEs to the European Medicines Agency (EMA) between 2011 and 2015 and their impact on the outcome of applications. It showed that SMEs experience challenges in the quality (e.g. manufacturing process validation and control and/or characterisation data of drug substance or drug product) and clinical sections of marketing authorisation applications (e.g. analysis or robustness of pivotal data or selection of submitted studies, study design issues and marginal or no clinical relevant efficacy), with deficiencies in demonstrating clinical efficacy representing the major eventual hurdles to authorisation.