BACKGROUND In addition to pressures typical of other medical professions, family physicians face additional challenges such as building long-term relationships with patients, dealing with patients' social problems, and working at a high level of uncertainty. We aimed to assess the rate of burnout and factors associated with it among family medicine residents throughout Israel. METHODS A cross sectional study based on a self-administered questionnaire. RESULTS Ninety family medicine residents throughout Israel completed the questionnaire. The rate of clinically significant burnout, assessed by the composite Shirom-Melamed Burnout Questionnaire score, was 14.4%. In univariate analyses several personal and professional characteristics, as well as all tested psychological characteristics, showed significant associations with burnout. However, in the multivariable logistic regression only psychological work-related characteristics (work engagement, psychological flexibility (reverse scoring), and perceived work-related stress) were significantly associated with burnout at OR (95% CI) = 0.23 (0.06-0.60), 1.31 (1.10-1.71), and 1.16 (1.05-3.749), respectively. CONCLUSIONS The integration of burnout prevention programs into academic courses during residency could explain the relatively low prevalence of burnout among family medicine residents in this study. Given the strong association of burnout with psychological characteristics, further investment in burnout prevention through targeted structured courses for residents should be encouraged.