Introduction: In connection with a government think tank's planned municipality reform, proposals have been made to separate the administration of the health care services so that general practice would be administered by the municipalities. The aim of this study was to elucidate general practitioners' contacts with the secondary health care sector and the municipalities. Materials and methods: For one week in September 2003, 295 general practitioners from five Danish counties registered all their contacts with the municipalities and the secondary health care system (7,565 contacts). The self-registration was done on a simple Audit Project Odense (APO) chart and supplemented with electronic communication data from MedCom for one county (Funen) and from the National Health Insurance. Results: More than 90% (95% CI: 90.5-91.7) of the contacts concerned the secondary health care system and less than 10% (95% CI: 8.3-9.5) the municipalities. The general practitioners considered medical expertise to be important in their contacts with both the secondary health care system and the municipalities, but more important in contacts with the former. Discussion: The study showed that the contacts involved primarily the secondary health care system. In relation to the gatekeeper function and the increasing focus on continuous episodes of care for individual patients, there may be still increasing demands for synergy between general practitioners and the secondary health care system. The collaboration on the municipality level will, however, also need to be strengthened.