Previous studies have reported that health sciences students are at greater risk for tuberculosis infection, especially in developing countries. The objective of this study was to estimate the prevalence, incidence, and factors associated with latent tuberculosis infection among Health Sciences students in Peru. Students enrolled at private university (in Lima – Peru) are tested annually for tuberculosis infection by tuberculin skin test. Data on tuberculin skin test results between 2002 and 2009 was used in this retrospective cohort study, a total of 4842 students were included. Tuberculin skin test conversion was defined as the change of tuberculin skin test from negative (<10 mm) to positive (≥10 mm) after 48–72 h of inoculation. Baseline tuberculin skin test positivity was 1.0% (95%CI: 0.6%–1.3%), whereas tuberculin skin test conversion incidence was 12.4 per 100 person-years (95%CI: 11.8–13.0). This study showed that students from clinical careers in close contact with patients had an increased risk of tuberculosis infection in the internship, especially Medicine, Dentistry, Medical Technology and Nursing. Administrative, environmental and personal protection measures should be implemented and evaluated periodically in order to reduce the risk of exposure.