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<h4>Background</h4>Hepatitis B is a global health problem. Trainees in the health-related fields are exposed to occupational risk of Hepatitis B Virus. In Uganda, there is scarcity of information on vaccination among students in health-care. The objective of this study was to assess hepatitis B vaccination status of the students and factors associated.<h4>Methods and findings</h4>This was a cross sectional study, conducted at Makerere University College of Health Sciences among undergraduate students who were eligible. A self-report on Hepatitis B vaccination status and various characteristics were collected on each participant, using a standardized structured self-administered questionnaire. Descriptive statistics were computed, bivariate and multivariate analysis were done using Stata 14.<h4>Results</h4>Out of 760 participants, 44.3% (95% CI 35.2-52.8) reported full vaccination. Vaccination was associated with gender, course, year of study and student's sponsorship. Males were less likely to be vaccinated, Prevalence Ratio (PR) 0.79; P-value <0.001, while self-sponsored students were also most likely to be vaccinated, PR 2.08; P-value <0.001. About 37% reported an accidental needle injury during their training.<h4>Conclusion</h4>Full vaccination was low and given the high prevalence of needle injuries, it raises a safety concern. Vaccination should be mandatory for all students prior to clinical exposure. There is need for targeted interventions to increase uptake.