Starting in 2009, the first ever Belgian nationwide data collection network using routine data extracted from primary care EPR (upload method) has been built from scratch. The network also uses a manual web-based data collection method. This paper compares these two methods by analysing missing and most recent values for certain parameters. We collected data from 4954 practices, pertaining to 29,180 patients. Mean values for the most recent parameters were similar regardless of which data collection method was used. Many missing recent values (>46%) were found for all of the parameters when using the upload method. It seems that, in Belgium, uploading routine data from primary care EPR on a large scale is suitable and allows the collection of chronological retrospective data. However, the method still requires major, carefully controlled improvements.