Key points * National Health Service (NHS) is becoming increasingly aware of the need to support independent research to answer some important questions for patient care in areas of scant commercial interest. * This article reports the main features and strategies of the independent research programme on drugs launched by the Italian Medicines Agency (AIFA) in 2005. * In the three bids launched between 2005 and 2007, a total of 151 studies have been approved for funding for a total of about 78 million Euro. * In this article we describe the Italian legislative framework under which the programme was launched, the types of research funded and discuss how the supported studies could contribute, in an international framework, to the knowledge needed on drug efficacy, effectiveness and safety.