BACKGROUND: Electronic health database (EHD) data is increasingly used by researchers. The major United Kingdom EHDs are the 'Clinical Practice Research Datalink' (CPRD), 'The Health Improvement Network' (THIN) and 'QResearch'. Over time, outputs from these databases have increased, but have not been evaluated. OBJECTIVE: This study compares research outputs from CPRD, THIN and QResearch assessing growth and publication outputs over a 10-year period (2004-2013). CPRD was also reviewed separately over 20 years as a case study. METHODS:  Publications from CPRD and QResearch were extracted using the Science Citation Index (SCI) of the Thomson Scientific Institute for Scientific Information (Web of Science). THIN data was obtained from University College London and validated in Web of Science. All databases were analysed for growth in publications, the speciality areas and the journals in which their data have been published. RESULTS: These databases collectively produced 1,296 publications over a ten-year period, with CPRD representing 63.6% (n=825 papers), THIN 30.4% (n=394) and QResearch 5.9% (n=77). Pharmacoepidemiology and General Medicine were the most common specialities featured. Over the 9-year period (2004-2013), publications for THIN and QResearch have slowly increased over time, whereas CPRD publications have increased substantially in last 4 years with almost 75% of CPRD publications published in the past 9 years. CONCLUSION: These databases are enhancing scientific research and are growing yearly, however display variability in their growth. They could become more powerful research tools if the National Health Service and general practitioners can provide accurate and comprehensive data for inclusion in these databases.