The purpose of the study was to determine the prevalence of the publication of a scientific article in an indexed journal by Peruvian doctors and its associated factors during the year 2016. An analysis was performed of secondary data from the National Healthcare User Satisfaction Survey (ENSUSALUD) 2016. The result variable was the publication of an article in an indexed journal from the Web of Science, Scopus or Medline, whereas the exposure variables were sociodemographic and academic. Means, standard deviation, frequencies, percentages, and chi-square and Student's t test were used to evaluate the differences in the publication of a scientific article. Crude and adjusted logistic regression models were developed. ENSUSALUD 2016 complex sampling was considered in all estimations. Data were obtained about 2 216 doctors, of whom 13.0% (CI 95%: 9.1-18.3) reported having published a scientific article in an indexed scientific journal. The adjusted model found an association between the publication of a scientific article and residence in Lima (OR: 0.30; CI 95%: 0.17-0.53), intermediate command of the English language (OR: 9.01; CI 95%: 2.24-36.70), advanced command of the English language (OR: 21.0; CI 95%: 4.74-93.12) and being a medical specialist (OR: 2.57; CI 95%: 1.08-6.12). The publication prevalence of a scientific article by Peruvian doctors is low. Residence in Lima, intermediate or advanced command of the English language, and being a medical specialist were factors associated to the publication of a scientific article.