Berkshire GP Dr Tim Walter and Glasgow GPSI Professor Aziz Sheikh will each receive a £10,000 grant towards their projects and access to the QResearch database.
The GPs won the inaugural awards from QResearch, a partnership between software company EMIS and the University of Nottingham.
Dr Walter's project will use the QDiabetes tool to improve detection of diabetes among 100,000 patients in the local CCG.
His aim is to develop a best practice toolkit to help other CCGs. Picking up more cases of undiagnosed diabetes would also raise QOF income.
Professor Sheikh, who works at the Royal Hospital for Sick Children in Edinburgh, will evaluate the safety of the smoking cessation drug varenicline among smokers with COPD or similar lung conditions. These patients may be more susceptible to possible side effects.
Professor Sheikh said: 'We are delighted to win this award and have the opportunity to work with QResearch data to answer a question of scientific and clinical importance.'
Dr Julia Hippisley-Cox, professor of clinical epidemiology and general practice at the University of Nottingham and co-founder of QResearch, said: 'Both projects demonstrated an innovative approach to two key issues for the NHS, based firmly in translating sound scientific study into outcomes that will benefit medical practitioners, patients and the general public - ultimately helping to improve UK health.'