Abstract Background In order to proceed from a paper based registration to a surveillance system that is based on extraction of electronic health records (EHR), knowledge is needed on the number and representativeness of sentinel GPs using a government-certified EHR system and the quality of EHR data for research, expressed in the compliance rate with three criteria: recording of home visits, use of prescription module and diagnostic subject headings. Methods Data were collected by annual postal surveys between 2005 and 2009 among all sentinel GPs. We tested relations between four key GP characteristics (age, gender, language community, practice organisation) and use of a certified EHR system by multivariable logistic regression. The relation between EHR software package, GP characteristics and compliance with three quality criteria was equally measured by multivariable logistic regression. Results A response rate of 99% was obtained. Of 221 sentinel GPs, 55% participated in the surveillance without interruption from 2005 onwards, i.e. all five years, and 78% were participants in 2009. Sixteen certified EHR systems were used among 91% of the Dutch and 63% of the French speaking sentinel GPs. The EHR software package was strongly related to the community and only one EHR system was used by a comparable number of sentinel GPs in both communities. Overall, the prescription module was always used and home visits were usually recorded. Uniform subject headings were only sometimes used and the compliance with this quality criterion was almost exclusively related to the EHR software package in use. Conclusions The challenge is to progress towards a sentinel network of GPs delivering care-based data that are (partly) extracted from well performing EHR systems and still representative for Belgian general practice.