BackgroundSwiss primary care (PC) is facing workforce shortage. Up to 2011 this workforce was supplied by two board certifications: general medicine and internal medicine. To strengthen them against subspecialties, they were unified into one: general internal medicine. However, since unification general practitioners’ career options are no longer restrained by early commitment to PC. This may lead to a decrease of future primary care physicians (PCPs).MethodsTo gain insights in timing and factors influencing career choice of internists, we addressed a cross sectional survey to all board certified internists in the years 2000–2010 (n = 1462). Main measures were: final career choice (PCPs, hospital internists or subspecialists), timing and factors influencing career choice, and attractiveness of PCP career during medical school and residency.ResultsResponse rate was 53.2%, 44.8% were female and median age was 45 years old. Final career choice was PCP for 39.1% of participants, 15.0% chose to become hospital internists, 41.8% became subspecialists and 4.0% other. Timing of career choice significantly differed between groups. Most of the subspecialists have chosen their career during residency (65.3%), while only 21.9% of the PCPs chose during residency. Work experience in an academic hospital was negatively associated with becoming PCP (P < 0.001). Family influence on career choice was more frequently reported among PCPs and chiefs’ influence more reported among non-PCPs (P < 0.001). Fifty-nine percent of the participants considered a career as PCP to be attractive during medical school, this proportion decreased over time.ConclusionsTiming of career choice of PCPs and subspecialists strongly differed. PCPs opted late for their career and potentially modifiable external factors seem to contribute to their decision. This stresses the importance of fostering attractiveness of PC during medical school as well as during and after residency and of tailored residency positions for future PCPs in the hospital-dominated new general internal medicine training.Electronic supplementary materialThe online version of this article (doi:10.1186/s12875-017-0624-2) contains supplementary material, which is available to authorized users.