The production of pharmaceuticals is one of the most highly regulated fields in terms of quality. The body of good manufacturing practice (GMP) represents the standard required by law; GMP embraces the guidelines that regulate all activities related to the production and quality control of medicinal products for human and veterinary use. This paper deals with the implementation of a quality management system (QMS) in compliance with GMP and ISO 9001 standards for the production and distribution of radiopharmaceuticals in a public research institute. The production of 2-[18F]fluoro-2-deoxy-d-glucose has been implemented according to GMP standards and has been licensed by the national Authority in 2007. In 2010, a project to orient the system’s GMP compliance to ISO 9001 standards has been approved. A QMS conforming to ISO 9001:2008 should be considered an important additional step in terms of quality, because ISO 9001 also takes into account economic and financial aspects, design and development aspects and introduces management review for measurement and analysis of the process with the aim of improving performances. The harmonization between GMP and ISO has been defined following the Pharmaceutical Quality System Q10 guideline developed by International Conference on Harmonization.