Objectives. To evaluate the frequency of publication and its associated factors by professors of scientific research in medical schools in Peru. Materials and methods. This was a cross-sectional study. We included all teachers of research courses from the 32 medical schools in Peru in 2011. The publication search was conducted using Google Scholar, Scopus and Medline. Both the crude and adjusted prevalence ratios (aPR) were calculated with confidence intervals at 95% using simple and multiple Poisson regression with robust variance. Results. Of the 201 university teachers, 43.8% had never published an article in a journal, 26.9% had an original article published in a journal indexed in Medline and 16.4% did so in the past two years. Only 3% had been corresponding authors in non-Peruvian, indexed journals Factors associated with having an original article published in Medline in the past two years were: being under 40 years of age (aPR 2.97, 95% CI: 1.21-7.32), being a professor at a university where a final thesis is required for graduation (aPR 8.84, 95% CI: 2.60-30.12) and working for a highly productive university (aPR 3.24, 95% CI: 1.03-10.20). Conclusions. The frequency of publication of research faculty in medical schools in Peru is low. Young university teachers and those working at scientifically productive universities were more likely to publish in an indexed journal.