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Background: The shortage and high turnover of physicians is a recurrent problem in health care systems; this is especially harmful to the expansion and full operation of primary health care (PHC). The aim of this paper is to analyze incidence and associated factors with physician turnover in primary health care services in the East Zone of São Paulo City.Methods: This is a retrospective cohort study of 1378 physicians over a 15 years' time period based on physicians' administrative records from two distinct secondary databases. Physicians' individual characteristics were analyzed including graduation and specialization. Survival analysis techniques such Kaplan-Meier and Cox Regression were used to analyze the termination of contract.Results: One thousand three hundred seventy-eight physicians were included in the study of which 130 [9.4%(CI95 8.0-11.1%)] remained in the PHC services. The mean and median time until the occurrence of the physician leaving the service was 2.14 years (CI95% 1.98-2.29 years) and 1.17 years [(CI95% 1.05-1.28 years)]. The probability of contract interruption was 45% in the first year and 68% in the second year. Independent factors associated with TEC were identified: workload of 40 h/week HR = 1.71 [(CI95% 1.4-2.09), p < 0.001]; initial salary ≤1052 BGI HR = 1.87 [(CI95 1.64-2.15), p < 0.001]; time since graduation ≤2 years HR =1.36 [(CI95 1.18-1.56), p < 0.001]; and the conclusion of residency in up to 3 years after leaving the service HR = 1.69 [(CI95 1.40-2.04), p < 0.001].Conclusions: The time of employment of the physician in PHC was relatively short, with a high probability of TEC in the first year. Modifiable factors such as working hours, starting salary, time since graduation from medical school and need to enter in a residency program were associated with TEC. In pointing out that modifiable factors are responsible for long term employment or the end of contract of physicians in PHC services of the Unified Health System in the periphery of a metropolitan area, the study provides support for the planning, implementation and management of policies and strategies aimed at attracting and retaining physicians in suburban, priority or underserved regions. [ABSTRACT FROM AUTHOR]