Abstract Background The aim of this research paper is to study job satisfaction of physicians and general practitioners at primary health care institutions during the health care reform in Lithuania. Methods Self-administrated anonymous questionnaires were distributed to all physicians and general practitioners (N = 243, response rate – 78.6%), working at Kaunas primary health care level establishments, in October – December 2003. Results 15 men (7.9%) and 176 women (92.1%) participated in the research, among which 133 (69.6%) were GPs and 58 (30.4%) physicians. Respondents claimed to have chosen to become doctors, as other professions were of no interest to them. Total job satisfaction of the respondents was 4.74 point (on a 7 point scale). Besides 75.5% of the respondents said they would not recommend their children to choose a PHC level doctor's profession. The survey also showed that the respondents were most satisfied with the level of autonomy they get at work – 5.28, relationship with colleagues – 5.06, and management quality – 5.04, while compensation (2.09), social status (3.36), and workload (3.93) turned to be causing the highest dissatisfaction among the respondents. The strongest correlation (Spearmen's ratio) was observed between total job satisfaction and such factors as the level of autonomy – 0.566, workload – 0.452, and GP's social status – 0.458. Conclusion Total job satisfaction of doctors working at primary health care establishments in Lithuania is relatively low, and compensation, social status, and workload are among the key factors that condition PHC doctors' dissatisfaction with their job.