Many medical schools require a student thesis before graduation. Publishing results in a peer-reviewed journal could be an indicator of scientific value and acceptability by the scientific community. The publication pattern of theses published by medical students in Peru is unknown. The aim of this study was to assess the characteristics and publication pattern of theses in biomedical-indexed journals conducted by medical students in a university with the highest research output in Peru. Data from registered theses between 2000 and 2003 were obtained from the university library. Publication of theses in biomedical journals was assessed in 2008 by a search strategy using PubMed, Google Scholar, LILACS, LIPECS and SciELO. Four hundred and eighty-two medical theses were registered between 2000 and 2003; 85 (17.6%) were published in biomedical-indexed journals. Of the published theses, 28 (5.8%) were published in MEDLINE-indexed journals, 55 (11.4%) in SciELO-indexed journals, 61 (12.6%) in LILACS-indexed journals and 68 (14.1%) in LIPECS-indexed journals. Most of the published theses (80%) were in Spanish and published in Peruvian journals; and 17 theses (20%) were published in foreign journals (all of them indexed in MEDLINE). In addition, 37 (43.5%) belong primarily to internal medicine, and 24 (28.2%) belong primarily to infectious diseases. Medical students were first authors in 71 (83.5%) of the articles. In this study, most of the published theses were in Spanish, published in local journals and indexed in LIPECS. The percentage of published theses in biomedical journals at this university is comparable with others coming from developed countries.