In order to determine the factors associated with publication practices used by physicians who work at hospitals from Cusco, Peru, an analytical cross-sectional study was conducted in the year 2014 which included all hospital physicians in the city. The bibliographic search was performed using the databases Google Scholar, SciELO, Medline and Scopus. Of the 414 physicians surveyed, 17 % had published an original paper in a scientific journal at least once in their lives, and 4 % had published a paper in a journal indexed in Scopus in the last three years. Physicians from Adolfo Guevara Velasco National Hospital showed the highest frequency of scientific publication (49 %). Original papers were the most commonly published type (69 %), whereas the field most frequently dealt with was medicine (51 %). Being a medical school teacher was a factor associated with having published an original paper during the three periods evaluated. Frequency of publication by physicians from hospitals in the city of Cusco, Peru, is low. However, physicians who teach at medical schools showed a higher probability of publishing in a journal indexed in Scopus.