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Objective The aim of this paper is to investigate how doctors working in primary health care in Latin American address patients with common mental disorders and to investigate how stigma can affect their clinical decisions. Methods Using a cross-sectional design, we applied an online self-administered questionnaire to a sample of 550 Primary Care Physicians (PCPs) from Bolivia, Brazil, Cuba and Chile. The questionnaire collected information about sociodemographic variables, training and experience with mental health care. Clinicians’ stigmatizing attitudes towards mental health were measured using the Mental Illness Clinicians' Attitudes Scale (MICA v4). The clinical decisions of PCPs were assessed through three clinical vignettes representing typical cases of depression, anxiety and somatization. Results A total of 387 professionals completed the questionnaires (70.3% response rate). The 63.7% of the PCPs felt qualified to diagnose and treat people with common mental disorders. More than 90% of the PCPs from Bolivia, Cuba and Chile agreed to treat the patients presented in the three vignettes. We did not find significant differences between the four countries in the scores of the MICA v4 stigma levels, with a mean = 36.3 and SD = 8.3 for all four countries. Gender (p = .672), age (p = .171), training (p = .673) and years of experience (p = .28) were unrelated to stigma. In the two multivariate regression models, PCPs with high levels of stigma were more likely to refer them to a psychiatrist the patients with depression (OR = 1.03, 95% CI, 0.99 to 1.07 p<0.05) and somatoform symptoms somatoform (OR = 1.03, 95% CI, 1.00 to 1.07, p<0.05) to a psychiatrist. Discussion The majority of PCPs in the four countries were inclined to treat patients with depression, anxiety and somatoform symptoms. PCPs with more levels of stigma were more likely to refer the patients with depression and somatoform symptoms to a psychiatrist. Stigmatizing attitudes towards mental disorders by